CCP-BioSim: Biomolecular Simulation at the Life Sciences Interface

Lead Research Organisation: University of Bristol
Department Name: Chemistry

Abstract

"Everything that living things do can be understood in terms of the jigglings and wigglings of atoms" as Richard Feynman provocatively stated nearly fifty years ago. But how can we 'see' this wiggling and jiggling and understand how it drives biology? Increasingly, computer simulations of biological macromolecules are helping to meet this challenge. Experiments can provide detailed structures of biological macromolecules such as proteins, but it is hard to study directly how the structures of individual molecules change on short timescales as they function. Similarly it is not yet possible to study directly by experiment alone the molecular mechanisms of fast processes such as chemical reactions in enzymes or ion transport through membranes. Simulations based on fundamental physics offer the potential of filling-in these crucial 'gaps', modelling how proteins and other biomolecules move, fluctuate, interact, react and function.
Physics-based simulations complement experiments in building a molecular level understanding of biology: they can test hypotheses and interpret and analyse experimental data in terms of interactions at the atomic level. A wide variety of simulation techniques have been developed, applicable to a range of different problems in biomolecular science. Simulations have already shown their worth in helping to analyse how enzymes catalyse biochemical reactions, and how proteins adopt their functional structures. They can help in the design of drugs and catalysts, and in understanding the molecular basis of disease. And simulations have played a key role in developing the conceptual framework now at the heart of biomolecular science, that is, the understanding that the way that biological molecules move and flex - their dynamics - is central to their function, demonstrating the truth of Feynman's assertion.
Developing methods from chemical physics and computational science will open exciting new opportunities in biomolecular science, including in drug design and development, synthetic biology, biotechnology and biocatalysis. Much biomolecular simulation demands HEC resources: e.g. large-scale simulations of biological machines such as the ribosome, proton pumps and motors, membrane receptor complexes and even whole viruses. A particular challenge is the integration of simulations across length and timescales: different types of simulation method are required for different types of problems). We work to develop 'multiscale' modelling and simulation methods to tackle these large problems, in areas such as drug metabolism and transport.

Planned Impact

Biomolecular simulation and modelling is vital e.g. to the pharmaceutical industry, where it is an integral part of drug design and development (e.g. in structure-based drug design and predictions of drug metabolism). Pharma needs well-trained scientists in this area, and new methods (e.g. for prediction of drug binding affinities). CCP-BioSim contributes directly to both of these key requirements. Our activities also promote collaboration between simulation and experiment; biomolecular simulation is central to multidisciplinary research programmes. CCP-BioSim, and the computational tools it develops and contributes to, increase biological applications of high-end computing (HEC). As well as biosimulation specialists, a broad community of industrial and academic bioscientists investigating biomolecular structure and function will benefit from CCP-BioSim. Longer term, CCP-BioSim has the potential to contribute to improvements in health and quality of life. The bioscience community will benefit through access to tools, training, and trained simulation specialists that enable novel and more effective multidisciplinary projects where computational methods enhance and extend their core experimental approaches. CCP-BioSim helps to train scientists able to work across the theory/experimental boundary. Impacts on health will come from the application of the methods fostered and disseminated by CCP-BioSim to drug design and discovery. CCP-BioSim will a) help to train new researchers b) develop and disseminate advanced computational methods and c) provide a forum to enhance industrial-academic research links (members of the management group have strong links with many pharmaceutical/biotech companies, e.g. AstraZeneca, Vernalis, Phaminox, GSK, Evotec, Pfizer, Sanofi, Astex, etc.). There is also broader impact of biomolecular simulation in areas such as drug delivery and synthetic biology. Finally, vast amounts of data are coming from genomics, proteomics, glycomics and structural biology. Developments in X-ray crystallography, high-throughput sequencing, protein production and crystallization, EM, SAXS, NMR and mass spectrometry, combined with modern data storage capacities have vastly increased the quantity of information available in structural biology, proteomics and genomics databases. Investment in understanding and interpretation in terms of biological function is vital to make use of this information. Biomolecular simulation is essential to enhance understanding and guide further experiments, especially as the quantity and complexity of biological data is immense and continues to grow. Improved understanding of biomolecular interactions and their consequences is not just of fundamental interest, but also benefits applied science. Progress in understanding biomacromolecules requires an integrated approach using a range of biophysical techniques, both experimental and computational. Biomolecular simulation will help to use these data to develop new drugs, catalysts and nanotechnology.

Publications

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Bueren-Calabuig JA (2016) Impact of Ser17 Phosphorylation on the Conformational Dynamics of the Oncoprotein MDM2. in Biochemistry

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Bunzel H (2020) Evolution of dynamical networks enhances catalysis in a designer enzyme

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Bunzel H (2022) Photovoltaic enzymes by design and evolution

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Bunzel HA (2021) Designing better enzymes: Insights from directed evolution. in Current opinion in structural biology

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Bunzel HA (2019) Emergence of a Negative Activation Heat Capacity during Evolution of a Designed Enzyme. in Journal of the American Chemical Society

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Bunzel HA (2021) Evolution of dynamical networks enhances catalysis in a designer enzyme. in Nature chemistry

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Buzas D (2023) In vitro generated antibodies guide thermostable ADDomer nanoparticle design for nasal vaccination and passive immunization against SARS-CoV-2 in Antibody Therapeutics

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Byrne MJ (2016) The Catalytic Mechanism of a Natural Diels-Alderase Revealed in Molecular Detail. in Journal of the American Chemical Society

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Calabrò G (2016) Elucidation of Nonadditive Effects in Protein-Ligand Binding Energies: Thrombin as a Case Study. in The journal of physical chemistry. B

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Caldwell TA (2022) Conformational dynamics of the membrane enzyme LspA upon antibiotic and substrate binding. in Biophysical journal

 
Title The Wasteland 
Description I. The Burial of the Dead April is the cruellest month, breeding Lilacs out of the dead land, mixing Memory and desire, stirring Dull roots with spring rain. Winter kept us warm, covering Earth in forgetful snow, feeding A little life with dried tubers. Summer surprised us, coming over the Starnbergersee With a shower of rain; we stopped in the colonnade, And went on in sunlight, into the Hofgarten, And drank coffee, and talked for an hour. Bin gar keine Russin, stamm' aus Litauen, echt deutsch. And when we were children, staying at the arch-duke's, My cousin's, he took me out on a sled, And I was frightened. He said, Marie, Marie, hold on tight. And down we went. In the mountains, there you feel free. I read, much of the night, and go south in the winter. What are the roots that clutch, what branches grow Out of this stony rubbish? Son of man, You cannot say, or guess, for you know only A heap of broken images, where the sun beats, And the dead tree gives no shelter, the cricket no relief, And the dry stone no sound of water. Only There is shadow under this red rock, (Come in under the shadow of this red rock), And I will show you something different from either Your shadow at morning striding behind you Or your shadow at evening rising to meet you; I will show you fear in a handful of dust. Frisch weht der Wind Der Heimat zu Mein Irisch Kind, Wo weilest du? "You gave me hyacinths first a year ago; "They called me the hyacinth girl." -Yet when we came back, late, from the Hyacinth garden, Your arms full, and your hair wet, I could not Speak, and my eyes failed, I was neither Living nor dead, and I knew nothing, Looking into the heart of light, the silence. Oed' und leer das Meer. Madame Sosostris, famous clairvoyante, Had a bad cold, nevertheless Is known to be the wisest woman in Europe, With a wicked pack of cards. Here, said she, Is your card, the drowned Phoenician Sailor, (Those are pearls that were his eyes. Look!) Here is Belladonna, the Lady of the Rocks, The lady of situations. Here is the man with three staves, and here the Wheel, And here is the one-eyed merchant, and this card, Which is blank, is something he carries on his back, Which I am forbidden to see. I do not find The Hanged Man. Fear death by water. I see crowds of people, walking round in a ring. Thank you. If you see dear Mrs. Equitone, Tell her I bring the horoscope myself: One must be so careful these days. Unreal City, Under the brown fog of a winter dawn, A crowd flowed over London Bridge, so many, I had not thought death had undone so many. Sighs, short and infrequent, were exhaled, And each man fixed his eyes before his feet. Flowed up the hill and down King William Street, To where Saint Mary Woolnoth kept the hours With a dead sound on the final stroke of nine. There I saw one I knew, and stopped him, crying: "Stetson! "You who were with me in the ships at Mylae! "That corpse you planted last year in your garden, "Has it begun to sprout? Will it bloom this year? "Or has the sudden frost disturbed its bed? "Oh keep the Dog far hence, that's friend to men, "Or with his nails he'll dig it up again! "You! hypocrite lecteur!-mon semblable,-mon frère!" II. A Game of Chess The Chair she sat in, like a burnished throne, Glowed on the marble, where the glass Held up by standards wrought with fruited vines From which a golden Cupidon peeped out (Another hid his eyes behind his wing) Doubled the flames of sevenbranched candelabra Reflecting light upon the table as The glitter of her jewels rose to meet it, From satin cases poured in rich profusion; In vials of ivory and coloured glass Unstoppered, lurked her strange synthetic perfumes, Unguent, powdered, or liquid-troubled, confused And drowned the sense in odours; stirred by the air That freshened from the window, these ascended In fattening the prolonged candle-flames, Flung their smoke into the laquearia, Stirring the pattern on the coffered ceiling. Huge sea-wood fed with copper Burned green and orange, framed by the coloured stone, In which sad light a carvéd dolphin swam. Above the antique mantel was displayed As though a window gave upon the sylvan scene The change of Philomel, by the barbarous king So rudely forced; yet there the nightingale Filled all the desert with inviolable voice And still she cried, and still the world pursues, "Jug Jug" to dirty ears. And other withered stumps of time Were told upon the walls; staring forms Leaned out, leaning, hushing the room enclosed. Footsteps shuffled on the stair. Under the firelight, under the brush, her hair Spread out in fiery points Glowed into words, then would be savagely still. "My nerves are bad tonight. Yes, bad. Stay with me. "Speak to me. Why do you never speak. Speak. "What are you thinking of? What thinking? What? "I never know what you are thinking. Think." I think we are in rats' alley Where the dead men lost their bones. "What is that noise?" The wind under the door. "What is that noise now? What is the wind doing?" Nothing again nothing. "Do "You know nothing? Do you see nothing? Do you remember "Nothing?" I remember Those are pearls that were his eyes. "Are you alive, or not? Is there nothing in your head?" But O O O O that Shakespeherian Rag- It's so elegant So intelligent "What shall I do now? What shall I do?" "I shall rush out as I am, and walk the street "With my hair down, so. What shall we do tomorrow? "What shall we ever do?" The hot water at ten. And if it rains, a closed car at four. And we shall play a game of chess, Pressing lidless eyes and waiting for a knock upon the door. When Lil's husband got demobbed, I said- I didn't mince my words, I said to her myself, HURRY UP PLEASE ITS TIME Now Albert's coming back, make yourself a bit smart. He'll want to know what you done with that money he gave you To get yourself some teeth. He did, I was there. You have them all out, Lil, and get a nice set, He said, I swear, I can't bear to look at you. And no more can't I, I said, and think of poor Albert, He's been in the army four years, he wants a good time, And if you don't give it him, there's others will, I said. Oh is there, she said. Something o' that, I said. Then I'll know who to thank, she said, and give me a straight look. HURRY UP PLEASE ITS TIME If you don't like it you can get on with it, I said. Others can pick and choose if you can't. But if Albert makes off, it won't be for lack of telling. You ought to be ashamed, I said, to look so antique. (And her only thirty-one.) I can't help it, she said, pulling a long face, It's them pills I took, to bring it off, she said. (She's had five already, and nearly died of young George.) The chemist said it would be all right, but I've never been the same. You are a proper fool, I said. Well, if Albert won't leave you alone, there it is, I said, What you get married for if you don't want children? HURRY UP PLEASE ITS TIME Well, that Sunday Albert was home, they had a hot gammon, And they asked me in to dinner, to get the beauty of it hot- HURRY UP PLEASE ITS TIME HURRY UP PLEASE ITS TIME Goonight Bill. Goonight Lou. Goonight May. Goonight. Ta ta. Goonight. Goonight. Good night, ladies, good night, sweet ladies, good night, good night. III. The Fire Sermon The river's tent is broken: the last fingers of leaf Clutch and sink into the wet bank. The wind Crosses the brown land, unheard. The nymphs are departed. Sweet Thames, run softly, till I end my song. The river bears no empty bottles, sandwich papers, Silk handkerchiefs, cardboard boxes, cigarette ends Or other testimony of summer nights. The nymphs are departed. And their friends, the loitering heirs of city directors; Departed, have left no addresses. By the waters of Leman I sat down and wept . . . Sweet Thames, run softly till I end my song, Sweet Thames, run softly, for I speak not loud or long. But at my back in a cold blast I hear The rattle of the bones, and chuckle spread from ear to ear. A rat crept softly through the vegetation Dragging its slimy belly on the bank While I was fishing in the dull canal On a winter evening round behind the gashouse Musing upon the king my brother's wreck And on the king my father's death before him. White bodies naked on the low damp ground And bones cast in a little low dry garret, Rattled by the rat's foot only, year to year. But at my back from time to time I hear The sound of horns and motors, which shall bring Sweeney to Mrs. Porter in the spring. O the moon shone bright on Mrs. Porter And on her daughter They wash their feet in soda water Et O ces voix d'enfants, chantant dans la coupole! Twit twit twit Jug jug jug jug jug jug So rudely forc'd. Tereu Unreal City Under the brown fog of a winter noon Mr. Eugenides, the Smyrna merchant Unshaven, with a pocket full of currants C.i.f. London: documents at sight, Asked me in demotic French To luncheon at the Cannon Street Hotel Followed by a weekend at the Metropole. At the violet hour, when the eyes and back Turn upward from the desk, when the human engine waits Like a taxi throbbing waiting, I Tiresias, though blind, throbbing between two lives, Old man with wrinkled female breasts, can see At the violet hour, the evening hour that strives Homeward, and brings the sailor home from sea, The typist home at teatime, clears her breakfast, lights Her stove, and lays out food in tins. Out of the window perilously spread Her drying combinations touched by the sun's last rays, On the divan are piled (at night her bed) Stockings, slippers, camisoles, and stays. I Tiresias, old man with wrinkled dugs Perceived the scene, and foretold the rest- I too awaited the expected guest. He, the young man carbuncular, arrives, A small house agent's clerk, with one bold stare, One of the low on whom assurance sits As a silk hat on a Bradford millionaire. The time is now propitious, as he guesses, The meal is ended, she is bored and tired, Endeavours to engage her in caresses Which still are unreproved, if undesired. Flushed and decided, he assaults at once; Exploring hands encounter no defence; His vanity requires no response, And makes a welcome of indifference. (And I Tiresias have foresuffered all Enacted on this same divan or bed; I who have sat by Thebes below the wall And walked among the lowest of the dead.) Bestows one final patronising kiss, And gropes his way, finding the stairs unlit . . . She turns and looks a moment in the glass, Hardly aware of her departed lover; Her brain allows one half-formed thought to pass: "Well now that's done: and I'm glad it's over." When lovely woman stoops to folly and Paces about her room again, alone, She smoothes her hair with automatic hand, And puts a record on the gramophone. "This music crept by me upon the waters" And along the Strand, up Queen Victoria Street. O City city, I can sometimes hear Beside a public bar in Lower Thames Street, The pleasant whining of a mandoline And a clatter and a chatter from within Where fishmen lounge at noon: where the walls Of Magnus Martyr hold Inexplicable splendour of Ionian white and gold. The river sweats Oil and tar The barges drift With the turning tide Red sails Wide To leeward, swing on the heavy spar. The barges wash Drifting logs Down Greenwich reach Past the Isle of Dogs. Weialala leia Wallala leialala Elizabeth and Leicester Beating oars The stern was formed A gilded shell Red and gold The brisk swell Rippled both shores Southwest wind Carried down stream The peal of bells White towers Weialala leia Wallala leialala "Trams and dusty trees. Highbury bore me. Richmond and Kew Undid me. By Richmond I raised my knees Supine on the floor of a narrow canoe." "My feet are at Moorgate, and my heart Under my feet. After the event He wept. He promised a 'new start.' I made no comment. What should I resent?" "On Margate Sands. I can connect Nothing with nothing. The broken fingernails of dirty hands. My people humble people who expect Nothing." la la To Carthage then I came Burning burning burning burning O Lord Thou pluckest me out O Lord Thou pluckest burning IV. Death by Water Phlebas the Phoenician, a fortnight dead, Forgot the cry of gulls, and the deep sea swell And the profit and loss. A current under sea Picked his bones in whispers. As he rose and fell He passed the stages of his age and youth Entering the whirlpool. Gentile or Jew O you who turn the wheel and look to windward, Consider Phlebas, who was once handsome and tall as you. V. What the Thunder Said After the torchlight red on sweaty faces After the frosty silence in the gardens After the agony in stony places The shouting and the crying Prison and palace and reverberation Of thunder of spring over distant mountains He who was living is now dead We who were living are now dying With a little patience Here is no water but only rock Rock and no water and the sandy road The road winding above among the mountains Which are mountains of rock without water If there were water we should stop and drink Amongst the rock one cannot stop or think Sweat is dry and feet are in the sand If there were only water amongst the rock Dead mountain mouth of carious teeth that cannot spit Here one can neither stand nor lie nor sit There is not even silence in the mountains But dry sterile thunder without rain There is not even solitude in the mountains But red sullen faces sneer and snarl From doors of mudcracked houses If there were water And no rock If there were rock And also water And water A spring A pool among the rock If there were the sound of water only Not the cicada And dry grass singing But sound of water over a rock Where the hermit-thrush sings in the pine trees Drip drop drip drop drop drop drop But there is no water Who is the third who walks always beside you? When I count, there are only you and I together But when I look ahead up the white road There is always another one walking beside you Gliding wrapt in a brown mantle, hooded I do not know whether a man or a woman -But who is that on the other side of you? What is that sound high in the air Murmur of maternal lamentation Who are those hooded hordes swarming Over endless plains, stumbling in cracked earth Ringed by the flat horizon only What is the city over the mountains Cracks and reforms and bursts in the violet air Falling towers Jerusalem Athens Alexandria Vienna London Unreal A woman drew her long black hair out tight And fiddled whisper music on those strings And bats with baby faces in the violet light Whistled, and beat their wings And crawled head downward down a blackened wall And upside down in air were towers Tolling reminiscent bells, that kept the hours And voices singing out of empty cisterns and exhausted wells. In this decayed hole among the mountains In the faint moonlight, the grass is singing Over the tumbled graves, about the chapel There is the empty chapel, only the wind's home. 
Type Of Art Creative Writing 
Impact Inspiration for grant applications and reporting in ResearchFish 
URL https://en.wikipedia.org/wiki/The_Waste_Land
 
Description Advisory team for UKRI review on impact of investment in HPC
Geographic Reach National 
Policy Influence Type Participation in a guidance/advisory committee
 
Description Future of HPC
Geographic Reach National 
Policy Influence Type Participation in a guidance/advisory committee
 
Description Research data and policy
Geographic Reach National 
Policy Influence Type Contribution to new or improved professional practice
URL https://www.chemistryworld.com/news/ukri-finds-itself-in-hot-water-too-over-researchfish-cyberbullyi...
 
Description UKRI research data capture approaches
Geographic Reach National 
Policy Influence Type Contribution to new or improved professional practice
URL https://www.researchprofessionalnews.com/rr-news-uk-research-councils-2023-1-researchfish-tweets-aga...
 
Description AMR Global Development Award 2017
Amount £88,000 (GBP)
Funding ID MR/R014922/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 10/2017 
End 03/2018
 
Description Action! Modelling DNA nano-machines for deciphering their molecular mechanisms
Amount £62,000 (GBP)
Funding ID EP/N509802/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 10/2019 
End 09/2022
 
Description AstraZeneca CASE studentship
Amount £29,500 (GBP)
Organisation AstraZeneca 
Sector Private
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End 02/2021
 
Description BBSRC Tools and Techniques: Computational tools for enzyme engineering: bridging the gap between enzymologists and expert simulation
Amount £146,027 (GBP)
Funding ID BB/L018756/1 
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Sector Public
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Description BBSRC sLoLa: Innovative Routes to Monoterpene Hydrocarbons and Their High Value Derivatives
Amount £3,038,984 (GBP)
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Sector Public
Country United Kingdom
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End 09/2019
 
Description BI - XChem
Amount £248,000 (GBP)
Organisation Boehringer Ingelheim 
Sector Private
Country Germany
Start 01/2019 
End 12/2020
 
Description BioNet - Dynamical Redesign of Biomolecular Networks
Amount £1,184,999 (GBP)
Funding ID 757850 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 02/2018 
End 01/2023
 
Description Biocatalysis and Biotransformation: A 5th Theme for the National Catalysis Hub
Amount £3,053,639 (GBP)
Funding ID EP/M013219/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 01/2015 
End 12/2019
 
Description BristolBridge has contributed to the University of Bristol being the UK's largest recipient of RCUK AMR cross-council funding awards both in number (7) and value (£5.268M). 6 related AMR grants awarded with BristolBridge PIs/Co-Is include MRC-led AMR.
Amount £5,268,000 (GBP)
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 10/2016 
End 09/2019
 
Description CCPBioSim: Biomolecular Simulation at the Life Science Interface
Amount £345,687 (FKP)
Funding ID EP/T026308/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 11/2020 
End 10/2025
 
Description Carbapenem Antibiotic Resistance in Enterobacteriaceae: Understanding Interactions of KPC Carbapenemases with Substrates and Inhibitors
Amount £668,396 (GBP)
Funding ID MR/T016035/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 01/2020 
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Description Center for Future Health Fund
Amount £13,000 (GBP)
Organisation University of York 
Sector Academic/University
Country United Kingdom
Start 06/2018 
End 09/2019
 
Description Confidence in Concept 'Developing a mobile device for rapid antimicrobial resistance detection in primary care'
Amount £74,685 (GBP)
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 06/2017 
End 05/2018
 
Description Development of physics-based computational models for predicting the spatial architecture of bacterial genomes
Amount £61,000 (GBP)
Funding ID EP/R513386/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 10/2017 
End 09/2020
 
Description Diet and Health Research Industry Club
Amount £398,037 (GBP)
Funding ID BB/M027449/1 and BB/M027597/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
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Description EPSRC
Amount £188,950 (GBP)
Funding ID E/EP/G007705/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
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Description EPSRC Flagship Software
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Description EPSRC Project Grant
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Funding ID EP/P011993/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
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Description IAA: Nucleoid-associated proteins in biofilms
Amount £17,000 (GBP)
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 01/2022 
End 07/2022
 
Description Industrial PhD studentship
Amount £30,000 (GBP)
Organisation Heptares Therapeutics Ltd 
Sector Private
Country United Kingdom
Start 03/2017 
End 02/2020
 
Description John Fell Fund
Amount £86,614 (GBP)
Organisation University of Oxford 
Sector Academic/University
Country United Kingdom
Start 09/2016 
End 12/2018
 
Description MPLS NIF FUND
Amount £8,420 (GBP)
Organisation University of Oxford 
Sector Academic/University
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Start 02/2017 
 
Description Oracle for Research Cloud Fellowship
Amount $100,000 (USD)
Organisation Oracle Corporation 
Sector Private
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Start 02/2023 
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Description PREDACTED Predictive computational models for Enzyme Dynamics, Antimicrobial resistance, Catalysis and Thermoadaptation for Evolution and Desig
Amount € 2,482,332 (EUR)
Funding ID 101021207 
Organisation European Research Council (ERC) 
Sector Public
Country Belgium
Start 10/2021 
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Description PhD studentships for overseas
Amount £64,900 (GBP)
Funding ID 625750 / 472433 
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Description RS Newton Fellowship
Amount £99,000 (GBP)
Funding ID NF171278 
Organisation The Royal Society 
Sector Charity/Non Profit
Country United Kingdom
Start 03/2018 
End 02/2020
 
Description Synthetic Biology Research Centre. BrisSynBio: Bristol Centre for Synthetic Biology
Amount £13,528,180 (GBP)
Funding ID BB/L01386X/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 07/2014 
End 07/2019
 
Description The UK High-End Computing Consortium for Biomolecular Simulation
Amount £321,432 (GBP)
Funding ID EP/R029407/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 11/2018 
End 10/2022
 
Description UKRI CoA Extension
Amount £24,675 (GBP)
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 10/2020 
End 01/2021
 
Description Understanding bacterial DNA gyrase for the development of novel antibiotics
Amount £65,000 (GBP)
Funding ID EP/W524657/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 09/2022 
End 09/2022
 
Description Understanding gating kinetics in Cys-loop receptors
Amount £345,655 (GBP)
Funding ID BB/S001247/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 11/2018 
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Description https://gtr.ukri.org/person/2A2990B1-E1E1-4888-8848-7C256C3A3B43
Amount £20,009,000 (GBP)
Funding ID https://gtr.ukri.org/person/2A2990B1-E1E1-4888-8848-7C256C3A3B43 
Organisation United Kingdom Research and Innovation 
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Title Bristol University uses Oracle Cloud Infrastructure to speed up smoking cessation drug discovery 
Description Scientists from the University of Bristol used Oracle Cloud Infrastructure to speed up research into how nicotine causes addiction by binding to specific receptors in the brain. 
Type Of Material Model of mechanisms or symptoms - human 
Year Produced 2019 
Provided To Others? Yes  
Impact Scientists at the University of Bristol have published research showing how nicotine affects receptors in the brain as part of an effort to design drugs that will help smokers to quit. They have done so using Oracle Cloud Infrastructure donated by the supplier and in collaboration with Achieve Life Sciences, a Seattle-based pharmaceutical company focused on the commercialisation of Cytisinicline, a plant-based alkaloid with a high binding affinity to the nicotinic acetylcholine receptor in the human brain. According to the US National Institute on Drug Abuse, the majority of smokers would like to stop smoking, and each year around half try to quit permanently. Yet, only about 6% of smokers are able to quit in any given year. Smoking is the second most common cause of death worldwide. The paper that issued from the Bristol research, A general mechanism for signal propagation in the nicotinic acetylcholine receptor family, was published in the Journal of the American Chemical Society in December 2019. Two of the authors are from Oracle's Cloud Development Centre in Bristol, Phil Bates and Gerardo Viedma Nunez. Adrian Mulholland from the University of Bristol's Centre for Computational Chemistry was co-lead author on the paper, along with Richard Sessions, senior research fellow at the School of Biochemistry at Bristol. Mulholland told Computer Weekly: "Our work shows how nicotine exerts its effects on nicotinic acetylcholine receptors. Understanding this should help us design better smoking cessation aids." The study, led by led University of Bristol scientists but involving academics from other institutions, used Oracle's cloud infrastructure. The researchers used new computational simulation methods to conduct 450 assessments of the biochemistry associated with the binding of nicotine to a subtype of nicotinic acetylcholine receptors, a mechanism believed to be responsible for the highly addictive nature of the drug. "Each simulation takes eight hours to run on a single cloud node", said Mulholland. "If we had used our own high-performance computing facility, it would have taken 90 days to do what we did in five. "We are lucky at Bristol to have pretty good HPC resources, but what the Oracle Cloud enabled us to do was to run a new class of simulation - 'non-equilibrium' simulations, of which there are hundreds that have to be done in parallel. The Oracle Cloud enabled us to run them in a matter of weeks, whereas it would otherwise have taken us a year. "To understand why nicotine is so addictive, and to develop molecules to help people quit smoking, we need to understand how nicotine affects the nervous system. By harnessing the power of cloud computing, we can quickly observe how nicotine exerts its effects at the molecular level. This information can inform future drug development of new treatments for companies like Achieve." According to a press statement from Achieve Life Sciences, Oracle and Bristol, the university and the pharmaceutical firm have teamed up to "formulate molecules and potential treatments to combat addiction and neurological disorders based on smoking cessation compound in development, cytisinicline". Cytisinicline is, according to the statement, a "plant-based alkaloid with a high binding affinity to the nicotinic acetylcholine receptor. It is believed to aid in smoking cessation by interacting with nicotine receptors in the brain by reducing the severity of nicotine withdrawal symptoms and by reducing the reward and satisfaction associated with smoking." The drug has been approved in Central and Eastern Europe for more than two decades, and has been used by "more than 20 million people", according to the press statement. The paper is one output of research originally funded by the EPSRC in 2016, with £724,000. Mulholland said the beauty of being able to use cloud computing for this sort of scientific research lies in its capacity to enable collaboration. "I'm a great believer in different sorts of scientists working together to get the best results. And that's not about computation in its own right, but as part of a product development programme," he said. "It's helping to inform what sort of molecules people might make to test as potential medicines. Being able to do the computational simulations fast enough so that scientists can design and adapt their experiments quickly should accelerate drug development. We couldn't have done this two years ago." The work brought together computational chemists, biochemists and research software engineers, working together to deploy the simulations of nicotine receptors. The computer simulations methodology used in this particular area of neuroscience could also, said Mulholland, be applied to the study of schizophrenia and Alzheimer's. 
URL https://www.computerweekly.com/news/252476773/Bristol-University-uses-Oracle-Cloud-Infrastructure-to...
 
Title SWISH a new Hamiltonian Replica Exchange-based computational algorithm 
Description We developed a novel and effective computational approach to predict cryptic binding sites on targets of pharmaceutical interest. 
Type Of Material Improvements to research infrastructure 
Year Produced 2016 
Provided To Others? Yes  
Impact The method has been described in an high-impact publication (JACS) and in a number of high-profile blogs in drug discovery. The PI has been invited by Pfizer and other pharmaceutical companies to give talks about the method. 
 
Title SlimMD 
Description This tool is a repository for sharing molecular dynamics trajectories developed by Sarah Harris and James Gebbie-Rayet. Biomolecular simulations are extremely computationally expensive, and so consume lots of energy when they run. We therefore need to make best use of them to respect our environment, so please do share and cite! The material in SlimMD has a maximum file size of 1GB and standard file formats and names making it easy to download and use. 
Type Of Material Improvements to research infrastructure 
Year Produced 2021 
Provided To Others? Yes  
Impact No impact has been reported yet, but this is expected to help with training and introducing new people to computational biology. It will be particullarly helpful for students on short projects who do not have the time or resources to run expensive simulations. 
URL https://www.ccpbiosim.ac.uk/slimmd
 
Title A Multiscale Workflow for Modelling Ligand Complexes of Zinc Metalloproteins 
Description Representative MD trajectories, topologies and input files for the protein:ligand complexes presented in the paper Yang et al. J Chem. Inf. Model. 2021. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Zinc metalloproteins are ubiquitous, with protein zinc centers of structural and functional importance, involved in interactions with ligands and substrates and often of pharmacological interest. Biomolecular simulations are increasingly prominent in investigations of protein structure, dynamics, ligand interactions, and catalysis, but zinc poses a particular challenge, in part because of its versatile, flexible coordination. A computational workflow generating reliable models of ligand complexes of biological zinc centers would find broad application. Here, we evaluate the ability of alternative treatments, using (nonbonded) molecular mechanics (MM) and quantum mechanics/molecular mechanics (QM/MM) at semiempirical (DFTB3) and density functional theory (DFT) levels of theory, to describe the zinc centers of ligand complexes of six metalloenzyme systems differing in coordination geometries, zinc stoichiometries (mono- and dinuclear), and the nature of interacting groups (specifically the presence of zinc-sulfur interactions). MM molecular dynamics (MD) simulations can overfavor octahedral geometries, introducing additional water molecules to the zinc coordination shell, but this can be rectified by subsequent semiempirical (DFTB3) QM/MM MD simulations. B3LYP/MM geometry optimization further improved the accuracy of the description of coordination distances, with the overall effectiveness of the approach depending upon factors, including the presence of zinc-sulfur interactions that are less well described by semiempirical methods. We describe a workflow comprising QM/MM MD using DFTB3 followed by QM/MM geometry optimization using DFT (e.g., B3LYP) that well describes our set of zinc metalloenzyme complexes and is likely to be suitable for creating accurate models of zinc protein complexes when structural information is more limited. 
URL https://data.bris.ac.uk/data/dataset/10p78zgsappbz226bzrdagabq9/
 
Title Atomic force microscopy and atomistic molecular dynamics simulation data to resolve structures of negatively-supercoiled DNA minicircles at base-pair resolution. 
Description Simulations results and data source of Figures published on Nature Communications 2021 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Available publicly. It is of interest of the research community 
URL https://springernature.figshare.com/articles/dataset/Atomic_force_microscopy_and_atomistic_molecular...
 
Title Atomic force microscopy and atomistic molecular dynamics simulation data to resolve structures of negatively-supercoiled DNA minicircles at base-pair resolution. 
Description This data record consists 2 zipped folders: Full AFM raw data set.zip, and Source data .zip.The zipped folder Full AFM raw data set.zip contains all raw AFM data including repeats and experiments carried out in alternative conditionsThe primary subfolder names correspond to the method of DNA immobilisation:Nickel - use of 3 mM NiCl2 in Ph7.4 20 mM HEPES bufferPLLNaOAc - use of PLL and pH 5.4 50 mM NaOAc bufferHR images - high resolution images, obtained also using the nickel conditions.The secondary subfolder names correspond to the superhelical density as shown in figure 3 in the article, and these contain the raw AFM images as .spm isles, the sub folders within those are created by the program TopoStats, and are processed data from the raw AFM images. File formats included in the zipped folder: .spm, .tiff, .json, .txt and .pdf.The zipped folder Source data .zip comprises all relevant data, pdbs of all the structures depicted in the paper obtained from simulations and AFM. See below for details on each sub folder within Source data 2.zip. Each folder contains the data used to generate each figure ad supplementary figure in the article. Figure 1: AFM data: the AFM raw files for the high-resolution images shown in figure 1, and calculations of their aspect ratios as aspectratiomanual.xlsxAFM movie: the AFM raw files for the time-lapse images shown in figure 1.MD data: the MD images used for the high-resolution images shown in figure 1 and .tar files - the MD files used to generate the snapshots MD movie: the MD snapshots files for the time-lapse images shown in figure 1 and .tar files - the MD files used to generate the snapshotsFile formats included in the Figure 1 sub folder: 0## files where ## represent numbers, .gwy, .txt, .eps, .mpg and .xlsx.Figure 2: Kink and defect measurements - the measured bend angles shown in Fig 2 and an AFM image showing how the FAM bends were measuredMD Radgyr Writhe - measurements of radius of gyrations and writhe for each topoisomer.tar files - the MD files used to generate the snapshots in 2a.txt file - the profile shown in fig 2bFile formats included in the Figure 2 sub folder: .tiff, .txt and .datFigure 3: The subfolder names correspond to the superhelical density as shown in figure 3, and these contain the raw AFM images as '.spm' isles, the sub folders within those are created by the program TopoStats, and are processed data from the raw AFM images. The '.json' file contains the data used to make the plots shown in Figure 3File formats included in the Figure 3 sub folder: .spm, .tiff, .txt, .json and .pdfFigure 4: '.dat' files contain information from MD simulations used to create the subfigure they are labelled with.The '.spm' and '.037' files are the raw AFM images used in this figure.The .tar files are MD simulations data used to generate the snapshots shown in figure 4.File formats included in the Figure 4 sub folder: .spm, .txt, .pdf and .datFigure S1: Simulations data generated using the SerraLine program, showing the average and maximum deviations from planarity in relative and absolute numbers.Data were plotted suing the distributions_plot.py script.File formats included in the Figure S1 sub folder: .csv, .pdf, and .txtFigure S2a: MD measurement of the writhe over time as a '.dat file' and snapshots as '.pdb' files. File formats included in the Figure S2a sub folder: .pdb and .dat.Figure S2b: MD measurement of the writhe over time as a '.dat file' and snapshots as '.pdb' files.File formats included in the Figure S2b sub folder: .pdb and .dat.Figure S3: The AFM and MD measurements of bending angles including all profiles for MD simulations, generated using Serraline A, FM images and measurements in the form '251angles' '339 angles'.File formats included in the Figure S3 sub folder: .tiff, .txt and .pdb.Figure S4: AFM length analysis of the position of the triplex on linearised minicircles. 'Csv' file contains the length data measured by hand using the IMOD software.Plots: plots of the data raw AFM data: AFM data files used in the analysisFile formats included in the Figure S4 sub folder: .csv, .xlsx, .pdf and 0## files where ## represent numbers.Figure S5: Surface plasmon resonance (SPR) data show the effect of ions on the affinity of the triplex for varying superhelical densities of DNA minicircles, plotted using the script 'sprplot'. '.pdf' files are the plots of the various excel files.File formats included in the Figure S5 sub folder: .json, .pdf and .xlsx.Figure S6: SPR data in showing the affinity of the triplex for varying superhelical densities of DNA minicircles, plotted using the script 'sprplot'. '.pdf' files are the plots of the various excel files.File formats included in the Figure S6 sub folder: .json, .pdf, .xlsx and .pdf.Figure S7: An MS '.tar' file containing the snapshots shown in figure S7File formats included in the Figure S7 sub folder: .pdbFigure S8: AFM data used in figure s8, the '.gwy' files are AFM images of the wide view, and each of the time-lapse images. The '.txt' files are the profiles taken in those images and plotted in the figure.File formats included in the Figure S8 sub folder: .gwy and .txt.Figure S9: Simulations data showing the difference between the OL$ and BSC1 forcefields.File formats included in the Figure S9 sub folder: .datSimulations: The simulations data File formats included in the Simulations sub folder: .gro and .xtcSupp videos: The supplementary videosFile formats included in the SuppVideods sub folder: .pdb and .mpgSoftware needed to access data: 20151103_251_NAT_17ng_Ni_20mm_052DX.058 or AFM_339_TFO_HR_cs.037, spm files & all files included in the "Raw AFM data" sub folder - Gwyddion, Nanoscope Analysiseps files - illustrator/ pdf software.mpg - any movie player.gro - gromacs files- GRO files may be viewed on a computer using a supporting HP calculator emulator, such as Emu48.xtc files - gromacs files- a suitable software like XTrkCADsee http://manual.gromacs.org/documentation/2018/user-guide/file-formats.html for more information on gromacs files.Study aims and methodology: In the cell, DNA is arranged into highly-organised and topologically-constrained (supercoiled) structures. It remains unclear how this supercoiling affects the detailed double-helical structure of DNA, largely because of limitations in spatial resolution of the available biophysical tools. In this study, the authors combined high-resolution atomic force microscopy (AFM) with molecular dynamics (MD) simulations to reveal how supercoiling affects global and local DNA conformation, structure and dynamics in DNA minicircles of length 250-340 bp. The following procedures are described in more detail in the related article: generation and purification of small DNA circles, preparation and analysis of different topological species of minicircles, S1 nuclease digestions, atomic force microscopy, atomistic simulations and surface plasmon resonance. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Used by the Stated Clearly website and YouTube channel to create the animation "What does DNA really look like?" for high school biology classes. Also used to create 3D models for the exhibition Materials Matter at the Sheffield Millennium Gallery 
URL https://springernature.figshare.com/articles/dataset/Atomic_force_microscopy_and_atomistic_molecular...
 
Title Evolution of dynamical networks enhances catalysis in a designer enzyme 
Description Data related to: "Evolution of dynamical networks enhances catalysis in a designer enzyme". H. Adrian Bunzel, J. L. Ross Anderson, Donald Hilvert, Vickery L. Arcus, Marc W. van der Kamp, Adrian J. Mulholland. Nature Chemistry 2021. MD Trajectories of a designed and evolved Kemp eliminase (1A53-2 and 1A53-2.5) in complex with a ground state (GS) or transition state (TS, TS2) model. The ligands are called GS1, TS1, and TS3 in the raw data. Cluster analysis of each trajectory, discriminating between an open (0) or closed (1) state for each frame. Pymol Sessions to reproduce Figures 1-3 of the paper. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Activation heat capacity is emerging as a crucial factor in enzyme thermoadaptation, as shown by the non-Arrhenius behaviour of many natural enzymes. However, its physical origin and relationship to the evolution of catalytic activity remain uncertain. Here we show that directed evolution of a computationally designed Kemp eliminase reshapes protein dynamics, which gives rise to an activation heat capacity absent in the original design. These changes buttress transition-state stabilization. Extensive molecular dynamics simulations show that evolution results in the closure of solvent-exposed loops and a better packing of the active site. Remarkably, this gives rise to a correlated dynamical network that involves the transition state and large parts of the protein. This network tightens the transition-state ensemble, which induces a negative activation heat capacity and non-linearity in the activity-temperature dependence. Our results have implications for understanding enzyme evolution and suggest that selectively targeting the conformational dynamics of the transition-state ensemble by design and evolution will expedite the creation of novel enzymes. 
URL https://data.bris.ac.uk/data/dataset/l6hm9j11yil92bh9rvh27i7ge/
 
Title IHF bends and bridges DNA in a multiplicity of states 
Description A representative pdb for each of the 4 topological states IHF induces in linear DNA 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact Structures obtained from simulations publicly available 
URL https://pure.york.ac.uk/portal/en/datasets/ihf-bends-and-bridges-dna-in-a-multiplicity-of-states(0b6...
 
Title MemProtMD 
Description a datbase of all membrane protein structures and their interactions with lipids 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact Considerable interest and uptake by membrane protein structural biologists in academia and industry (pharma). 
URL http://memprotmd.bioch.ox.ac.uk
 
Title SWISH a new Hamiltonian Replica Exchange-based computational algorithm 
Description We developed a novel and effective computational approach to predict cryptic binding sites on targets of pharmaceutical interest. 
Type Of Material Computer model/algorithm 
Year Produced 2016 
Provided To Others? Yes  
Impact The method has been described in an high-impact publication (JACS) and in a number of high-profile blogs in drug discovery. The PI has been invited by Pfizer and other pharmaceutical companies to give talks about the method. 
 
Title Simulation of Functional Motions in Enzymes 
Description Data related to: "Structure and function in homodimeric enzymes: simulations of cooperative and independent functional motions". Wells SA, Van der Kamp MW, Mulholland AJ. PLOS ONE, 2015. Results from two different simulation methods, normal-mode biased geometric simulations of flexible motion and conventional molecular dynamics, as applied to two different homodimeric enzymes, the DcpS scavanger decapping enzyme and citrate synthase. 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact Large-scale conformational change is a common feature in the catalytic cycles of enzymes. Many enzymes function as homodimers with active sites that contain elements from both chains. Symmetric and anti-symmetric cooperative motions in homodimers can potentially lead to correlated active site opening and/or closure, likely to be important for ligand binding and release. Here, we examine such motions in two different domain-swapped homodimeric enzymes: the DcpS scavenger decapping enzyme and citrate synthase. We use and compare two types of all-atom simulations: conventional molecular dynamics simulations to identify physically meaningful conformational ensembles, and rapid geometric simulations of flexible motion, biased along normal mode directions, to identify relevant motions encoded in the protein structure. The results indicate that the opening/closure motions are intrinsic features of both unliganded enzymes. In DcpS, conformational change is dominated by an anti-symmetric cooperative motion, causing one active site to close as the other opens; however a symmetric motion is also significant. In CS, we identify that both symmetric (suggested by crystallography) and asymmetric motions are features of the protein structure, and as a result the behaviour in solution is largely non-cooperative. The agreement between two modelling approaches using very different levels of theory indicates that the behaviours are indeed intrinsic to the protein structures. Geometric simulations correctly identify and explore large amplitudes of motion, while molecular dynamics simulations indicate the ranges of motion that are energetically feasible. Together, the simulation approaches are able to reveal unexpected functionally relevant motions, and highlight differences between enzymes. 
URL http://data.bris.ac.uk/data/dataset/1klro7qjw27xi19qrcs1bb2nt6/
 
Title Simulations of circular RNAs from the Rolling Circle RNA synthesis 
Description All-atom trajectories from simulations done over the different stages of Rolling Circle RNA synthesis 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact None 
URL https://pure.york.ac.uk/portal/en/datasets/b92977bd-f016-4740-8b4a-f86c68d5eb2c
 
Title Simulations of supercoiled minicircles bound to IHF 
Description Trajectories for all-atom simulations pf DNA minicircles bound to the bacterial protein IHF 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
Impact None 
 
Title agnesnoy/SerraLINE: SerraLINE v1.0 
Description Version utilized in the paper: ALB Pyne, A Noy, K Main, V Velasco-Berrelleza, MM Piperakis, LA Mitchenall, FM Cugliandolo, JG Beton, CEM Stevenson, BW Hoogenboom, AD Bates, A Maxwell, SA Harris (2020). "Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and recognition", Accepted in Nat Commun 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact None 
URL https://zenodo.org/record/4105979
 
Title agnesnoy/SerraNA: SerraNA v1.0 
Description By Victor Velasco-Berrelleza and Agnes Noy Published at: V Velasco-Berrelleza, M Burmann, JW Shepherd, MC Leake, R Golestanian, A Noy (2020). "SerraNA: a program to determine nucleic acids elasticity from simulation data" Phys Chem Chem Phys, 22, 19254-19266 https://doi.org/10.1039/D0CP02713H 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact None 
URL https://zenodo.org/record/4105986
 
Title agnesnoy/WrLINE: WrLINEv1.0 
Description By Thana Sutthibutpong and Agnes Noy Published at: Sutthibutpong T, Harris SA, Noy A* (2015). "Comparison of molecular contours for measuring writhe in atomistic supercoiled DNA" J Chem Theor Comput, 11, 2768. DOI:10.1021/acs.jctc.5b00035 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact None 
URL https://zenodo.org/record/4106245
 
Description Catalysis Hub 
Organisation Research Complex at Harwell
Department UK Catalysis Hub
Country United Kingdom 
Sector Public 
PI Contribution Modelling and simulation of enzyme mechanisms for applications in biocatalysts via the Catalysis Hub
Collaborator Contribution Modelling and simulation of enzyme mechanisms for applications in biocatalysts via the Catalysis Hub and training of Hub PDRAs.
Impact Catalysis is a core area of contemporary science posing major fundamental and conceptual challenges, while being at the heart of the chemical industry - an immensely successful and important part of the overall UK economy (generating in excess of £50 billion per annum). UK catalytic science currently has a strong presence, but there is intense competition in both academic and industrial sectors, and a need for UK industrial activity to shift towards new innovative areas posing major challenges for the future. In light of these challenges the UK Catalysis Hub endeavours to become a leading institution, both nationally and internationally, in the field and acts to coordinate, promote and advance the UK catalysis research portfolio. With a strong emphasis on effective use of the world-leading facilities on the RAL campus. Structure The project has four mature themes and a fifth theme starting in 2015 , each with a lead investigator as PI - Catalysis by Design (Catlow); Energy (Hardacre); Environment (Hutchings); Chemical Transformations (Davidson) and the new Biocatalysis and Biotransformations (Nick Turner Manchester) - with the design theme based in the Harwell hub. Each theme is supported by £3 - 3.5M EPSRC funding over 5 years and within each theme there are typically six to eight sub-projects funded initially for 2 years, involving collaborative teams working at a variety of sites throughout the UK. Professor Hutchings acts as director of the whole national programme for the first three year period and chairs the management group, which is supported by a steering group and an industrial advisory panel. We note that engagement with industry is one of the key aims of the catalysis hub project. As well as hosting the design theme, the centre within the Research Complex at Harwell (RCaH) will coordinate the programme, be a base for national and international visitors and provide both training and outreach activities.
Start Year 2015
 
Description Collaboration with Beata Vertessy 
Organisation Budapest University of Technology and Economics
Department Department of Biotechnology and Food Sciences
Country Hungary 
Sector Academic/University 
PI Contribution We initiated a collaborative project to studey the role of conserved arginine residues in the dUTPase enzyme. We first performed a PDB-side structural analysis to compare arginine residues in NTP cleaving enzymes. Subsequently, we carried out QM/MM and MD calculations to establish the function of the key arginine finger residue in dUTPases.
Collaborator Contribution In this collaboration the experimental group led by Beata Vertessy performed X-Ray crystallography experiments togeter with biochemical experiments to use this in our joint project.
Impact Nagy et al, Journal of the American Chemical Society, 2016, DOI: 10.1021/jacs.6b09012 Multidisciplinary collaboration with experimental X-Ray crystallography and biochemistry group and our theoretical and computational biophysical chemistry group.
Start Year 2014
 
Description Collaboration with Bristol university on predicting drug-target binding kinetics 
Organisation University of Bristol
Department School of Chemistry
Country United Kingdom 
Sector Academic/University 
PI Contribution We contributed our enhanced sampling simulation algorithms including TS-PPTIS. Our approach will be combined with Prof. Mulholland's QM/MM algorithms to accurately predict binding kinetics.
Collaborator Contribution Prof. Mulholland's contributed his QMMM algorithms as well as Waterswap to the combined computational platform.
Impact A combined computational platform to predict binding kinetics and model the transition state ensemble.
Start Year 2015
 
Description Collaboration with CCP-EM/CCP4 for gylcosylated proteins 
Organisation York Structural Biology Laboratory (YSBL)
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution I share knowledge about molecular simulations (including visiting York and giving a talk).
Collaborator Contribution They contribute knowlege about glycans and structural biology.
Impact no publications yet
Start Year 2019
 
Description Collaboration with Derick Rousseau 
Organisation Ryerson University
Country Canada 
Sector Academic/University 
PI Contribution Coarse-grained molecular simulation of monoglyceride self-assembly at triglyceride-water and air-water interfaces.
Collaborator Contribution Experimental studies on the molecular templating effect of monoglycerides on triglyceride crystallization at oil-water interfaces
Impact A poster and oral presentation was given at Food Colloids 2016 held at Wageningen university the Netherlands. A manuscript has been submitted and is under review.
Start Year 2016
 
Description Collaboration with Dr. Alice Pyne, University of Sheffield 
Organisation Henry Royce Institute
Department Henry Royce Institute – University of Sheffield Facilities
Country United Kingdom 
Sector Academic/University 
PI Contribution Intellectual input and expertise, time of PhD student and access to data
Collaborator Contribution Access to the Henry Royce center through a participation scheme with time dedicated from the Research Officer and in kind materials
Impact -Article in Nature Communications, DOI: 10.1038/s41467-021-21243-y -Articles in Media: Daily Express, Daily Mail, Yahoo News and Deccan Herald -Interviews in Media: Alice Pyne at ITV
Start Year 2016
 
Description Collaboration with Dr. Tung Le, JIC, Norwich 
Organisation John Innes Centre
Country United Kingdom 
Sector Academic/University 
PI Contribution Expertise and PhD student time to perform MD simulations that support the experiments
Collaborator Contribution They provide the experimental structures
Impact A publication in Cell Reports (2020), DOI: 10.1016/j.celrep.2020.107928
Start Year 2019
 
Description Collaboration with Johnson and Johnson 
Organisation Johnson & Johnson
Department Janssen-Cilag
Country Global 
Sector Private 
PI Contribution We helped J & J implement a computational pipeline for cryptic binding pocket discovery and collaborated on looking for druggable cryptic binding pockets on targets such the IMPase.
Collaborator Contribution Provided interesting drug targets and experimental data, including NMR fragment screening.
Impact Found interesting cryptic pockets in IMPase
Start Year 2020
 
Description Collaboration with Paul Clegg 
Organisation University of Edinburgh
Country United Kingdom 
Sector Academic/University 
PI Contribution This project was collaborative with UoE who provided experimental expertise to complement computer modelling at HWU.
Collaborator Contribution Provided expertise in soft matter physics, atomic force microscopy, spectroscopy.
Impact We have authored 5 papers (6th in preparation). These are listed under this award.
Start Year 2016
 
Description Collaboration with Prof. Anthony Maxwell, JIC, Norwich and Inspiralis 
Organisation John Innes Centre
Country United Kingdom 
Sector Academic/University 
PI Contribution Performed simulations and write a CASE studentship
Collaborator Contribution He put us in contact with the company Inspiralis
Impact CASE studentship: EP/W524657/1
Start Year 2021
 
Description Collaboration with Prof. Fred Antson (York) and Cyril Sanders (Sheffield) 
Organisation University of Sheffield
Department Sheffield Medical School
Country United Kingdom 
Sector Academic/University 
PI Contribution Secure a PhD studentship
Collaborator Contribution Share data and expertise
Impact Shared PhD student ship (EP/N509802/1) Manuscript in preparation
Start Year 2017
 
Description Collaboration with Prof. Jose Maria Lluch's group 
Organisation Autonomous University of Barcelona (UAB)
Country Spain 
Sector Academic/University 
PI Contribution We helped to carry out and analyse QM/MM MD simulations using umbrella sampling bias, and calculated the kinetics as well as the free energies of the catalytic reaction to obtain the Arrhenius prefactor.
Collaborator Contribution Patricia Laura, a PhD student was awarded funding to visit my group and work in my lab.
Impact Joint publication by Suardiaz et al, J. Chem. Theor. Comput. 2016, DOI: 10.1021/acs.jctc.5b01236.
Start Year 2015
 
Description Collaboration with Prof. Lynn Zechiedrich, Baylor College of Medicine, and Twister Biotech, USA 
Organisation Baylor College of Medicine
Country United States 
Sector Hospitals 
PI Contribution Leading the project and providing the PhD students for doing simulations and experiments
Collaborator Contribution Synthesis of DNA minicircles
Impact As a result of this collaboration we have DNA minicircles for performing experiments
Start Year 2018
 
Description Collaboration with Prof. Lynn Zechiedrich, Baylor College of Medicine, and Twister Biotech, USA 
Organisation Twister Biotech
Country United States 
Sector Private 
PI Contribution Leading the project and providing the PhD students for doing simulations and experiments
Collaborator Contribution Synthesis of DNA minicircles
Impact As a result of this collaboration we have DNA minicircles for performing experiments
Start Year 2018
 
Description Collaboration with Prof. Phil Holliger, MRC-LMB, Cambridge 
Organisation Medical Research Council (MRC)
Department MRC Laboratory of Molecular Biology (LMB)
Country United Kingdom 
Sector Academic/University 
PI Contribution Expertise and time to perform MD simulations that support the experiments
Collaborator Contribution Intellectual contribution and expertise on evolutionary molecular biology
Impact Publication in eLIFE, 2022 with more than 10 citations in a year, DOI: 10.7554/eLife.75186
Start Year 2021
 
Description Collaboration with SANOFI and Evotec on the allosteric regulation of receptor Tyrosine kinases. 
Organisation Evotec
Country Germany 
Sector Private 
PI Contribution In this successful partnership, we helped designing a new class of allosteric anticancer drugs by using our novel computational algorithms to sample rare events and predict binding kinetics.
Collaborator Contribution The partners contributed to the success of the research by performing large scale ligand screening ad providing high resolution crystallographic structures and biophysical data on the ligand-target complex.
Impact A novel allosteric inhibitor is in re-clinical development for cancer.
Start Year 2015
 
Description Collaboration with SANOFI and Evotec on the allosteric regulation of receptor Tyrosine kinases. 
Organisation Sanofi
Department Aventis
Country France 
Sector Private 
PI Contribution In this successful partnership, we helped designing a new class of allosteric anticancer drugs by using our novel computational algorithms to sample rare events and predict binding kinetics.
Collaborator Contribution The partners contributed to the success of the research by performing large scale ligand screening ad providing high resolution crystallographic structures and biophysical data on the ligand-target complex.
Impact A novel allosteric inhibitor is in re-clinical development for cancer.
Start Year 2015
 
Description Collaboration with UCB pharma on cryptic sites 
Organisation UCB Pharma
Country United Kingdom 
Sector Private 
PI Contribution We contributed our new computational methods to find cryptic binding sites.
Collaborator Contribution Experimental validation, including crystal structures, surface plasmon resonance, new compounds.
Impact Helped develop new drug candidates.
Start Year 2018
 
Description Developing new computational approaches to inhibit "undruggable" targets. 
Organisation UCB Pharma
Country United Kingdom 
Sector Private 
PI Contribution We shared with UCB early versions of a computational platform we are developing to target allosteric sites on otherwise "undruggable" targets, i.e. pharmaceutical targets that are difficult to target with traditional drug design approaches based on substrate competitive ligands.
Collaborator Contribution UCB contributed to the project with high quality structural and biological data and is hiring a dedicated PDRA to work on the collaboration for 3 years.
Impact The new tools have been used to design novel drugs.
Start Year 2016
 
Description Evotec AI 
Organisation Evotec (UK) Ltd
Country United Kingdom 
Sector Private 
PI Contribution Studentship aimed at researching the use of MD in Artificial Intelligence.
Collaborator Contribution None yet.
Impact N/A yet.
Start Year 2018
 
Description Industrial collaboration with EVOTEC 
Organisation Evotec
Country Germany 
Sector Private 
PI Contribution We helped EVOTEC to rationalize the binding mode of a novel allosteric modulator of FGFR. By using our novel "SWISH" Hamiltonian Replica exchange algorithm, we predicted a previously unknown binding cavity in the D3 domain of FGFR3c, which was then validated by NMR spectroscopy.
Collaborator Contribution Evotec provided a plethora of unpublished experimental data on the binding mode and on the biological effect of the new tool compound in cells.
Impact The collaboration is multi-disciplinary involving Computational Chemistry, Chemical Biology, Structural Biology, Cellular Biology and Drug Discovery. A new manuscript is in preparation and will soon be submitted to a very prominent and high-impact journal. The PI (FLG) has been invited to a number of high-profile national international (ACS-meeting) conferences to discuss the results.
Start Year 2016
 
Description MARISURF 
Organisation Marlow Foods
Country United Kingdom 
Sector Private 
PI Contribution MARISURF is a 4.8Meuro H2020 project coordinated by HWU to identify, isolate and purify biosurfactants from marine bacteria. The production will then be scaled up to pilot scale and the surfactants tested by industrial end-users from various industry sectors including food, cosmetic and biomedical sectors. My research group is responsible for overall coordination of the project, and specifically for the screening of functional properties of the surfactants to ensure suitability in industrial applications.
Collaborator Contribution Marlow Foods are a partner in MARISURF an EUH2020 project coordinated by HWU. They will test marine bacteria-derived surfactants in their Quorn food applications.
Impact The collaboration is multi-disciplinary and involves the following scientific disciplines, Microbiology Chemistry Biochemistry Molecular Biology Process Engineering
Start Year 2015
 
Description Modelling of enzyme catalysed reaction mechanisms relevant to pharmaceutical development 
Organisation Pfizer Ltd
Country United Kingdom 
Sector Private 
PI Contribution Confidential
Collaborator Contribution Confidential
Impact Confidential
Start Year 2011
 
Description Organic synthesis of alternative gelator molecules 
Organisation Heriot-Watt University
Department Department of Mathematics
Country United Kingdom 
Sector Academic/University 
PI Contribution Shared information on olegelation. Invited collaborator to project meetings. Eventual joint publications.
Collaborator Contribution The partner will synthesize a range of alternative olegelator molecules that are derivatives of gamma oryzanol that either have the ferullic acid side chain substituted for another group, or have a hydroxyl group substituted. The hydroxyl group is believed to be important in dimerization of the sterols prior to their subsequent self-association into tubules, and also stabilizes the tubules through cooperative H-bonding. The ferrulic acid group is believed to allow inter-tubule interaction (it sticks out from the surface of the tubule) via pi-pi stacking interactions, thus leading to gel formation. By creating and testing oleogelators where one or both of these groups has been substituted will allow us to understand the role they play in the self-association and gelation process.
Impact Too early in project/collaboration.
Start Year 2017
 
Description Participation of European Topology interdisciplinary Initiative (Eutopia) network 
Organisation European Cooperation in Science and Technology (COST)
Department COST Action
Country Belgium 
Sector Public 
PI Contribution I gave a talk and exchanged views and knowledge with scientific colleagues
Collaborator Contribution The network invited me to give a talk
Impact I gave a talk to the 2nd annual meeting of the network It is a multidisciplinary network from mathematics to biology, physics and chemistry.
Start Year 2019
 
Description Vertex - CFTR 
Organisation Vertex Pharmaceuticals
Country United States 
Sector Private 
PI Contribution This is a studentship that will commence in 2019.
Collaborator Contribution None yet.,
Impact N/A.
Start Year 2019
 
Description collaboration with Novartis 
Organisation Novartis
Department Drug Discovery & Development
Country United States 
Sector Private 
PI Contribution We have shared data and software/home-made code to derive kinetic rates from umbrella sampling simulations. We also developed methods to be used for calculating residence times frlom atomistic simulations.
Collaborator Contribution Shared data with us of atomistic simulations for drug molecules crossing the membrane.
Impact We have joint publications.
Start Year 2018
 
Description collaboration with Walter Kolch 
Organisation University College Dublin
Country Ireland 
Sector Academic/University 
PI Contribution Computational MD simulations to reveal structure and dynamics of RAF kinases.
Collaborator Contribution Prof. Kolch's group carried out in vitro and in cell biochemical experiments to reveal RAF kinase activity and validate key mutations suggested by computational results.
Impact Jambrina et al, Angewandte Chemie, 2016, DOI: 10.1002/anie.201509272 Sanchez-Sanz et al, PLOS Computational Biology, 2016, DOI: 10.1371/journal.pcbi.1005051 Interdisciplinary research with essential biochemical and biological experiments from the Kolch group (Systems Biology Ireland) and computational work from our group.
Start Year 2012
 
Description water network analysis 
Organisation University of Oxford
Department Department of Biochemistry
Country United Kingdom 
Sector Academic/University 
PI Contribution Training and insights related to our methods.
Collaborator Contribution Partners provided the data and and associated collaborators for us to use in our analysis.
Impact Paper reporting collaboration results published,
Start Year 2016
 
Title APPARATUS FOR AND METHOD OF PROCESSING BIOLOGICAL SAMPLES 
Description The present invention provides systems, devices, apparatuses and methods for automated bioprocessing. Examples of protocols and bioprocessing procedures suitable for the present invention include but are not limited to: immunoprecipitation, chromatin immunoprecipitation, recombinant protein isolation, nucleic acid separation and isolation, protein labeling, separation and isolation, cell separation and isolation, food safety analysis and automatic bead based separation. In some embodiments, the invention provides automated systems, automated devices, automated cartridges and automated methods of western blot processing. Other embodiments include automated systems, automated devices, automated cartridges and automated methods for separation, preparation and purification of nucleic acids, such as DNA or RNA or fragments thereof, including plasmid DNA, genomic DNA, bacterial DNA, viral DNA and any other DNA, and for automated systems, automated devices, automated cartridges and automated methods for processing, separation and purification of proteins, peptides and the like. 
IP Reference US2018111121 
Protection Patent application published
Year Protection Granted 2018
Licensed Yes
Impact the patent has been instrumental for the incorporation of the spin out company Vitamica Ltd
 
Title METHOD AND APPARATUS FOR BACTERIAL ANALYSIS 
Description An apparatus (10) comprising: a light source (12); to cast light toward a substrate (20) defining a bacteria binding volume to create an evanescent field (22), the bacteria binding volume being within the evanescent field; a detector (32, 34) arranged to receive light from the bacteria binding volume and output data (36, 37); and a processor (38) arranged to determine vibration of bacteria (26) within the bacteria binding volume in three-dimensions from the data. 
IP Reference WO2019025771 
Protection Patent application published
Year Protection Granted 2019
Licensed Yes
Impact The patent has being instrumental for the incorporation of the spin out company Vitamica Ltd.
 
Title METHOD FOR DETECTION OF INTESTINAL, AND BLOOD-BRAIN BARRIER PERMEABILITY AND TESTING MATERIALS THERETO 
Description METHOD FOR DETECTION OF INTESTINAL, AND BLOOD-BRAIN BARRIER PERMEABILITY AND TESTING MATERIALS THERETO Methods, assays, and apparatus are disclosed for testing of antigens associated with intestinal and/or blood-brain barrier permeability. For example, blood, saliva or other bodily fluid can be tested for binding (1) to a bacterial toxin (preferably a lipopolysaccharide), and (2) binding to tissue antigens selected from at least one of (a) a gut-related antigen and (b) a blood brain barrier-related antigen. Analysis of test results can be used to assist in detecting and diagnosing diseases associated with leaky gut syndrome (whether due to paracellular or transcellular pathways, and whether due to bacterial toxins or some other cause) and/or to diseases associated with excessive blood brain barrier permeability, which are contemplated herein to include both neuroinflammation and/or neuroautoimmunity conditions, and especially amyotrophic lateral sclerosis, Parkinsons disease, multiple sclerosis, Alzheimer's, or peripheral neuropathy, and major depression. 
IP Reference AU2016259430 
Protection Patent application published
Year Protection Granted 2016
Licensed Yes
Impact the patent has been instrumental for the incorporation of the spin out company Vitamica Ltd
 
Title BioSimSpace 
Description BioSimSpace is an interoperable Python framework for biomolecular simulation. It is the Flagship Software Development Project of CCP-BioSim. With it you can: -Write robust and portable biomolecular workflow components that work on different hardware, with different software packages, and that can be run in different ways, e.g. command-line, Jupyter. -Interact with running molecular simulation processes in real-time. BioSimSpace is a new software framework to create an interoperability layer around the many software packages that are already embedded within the biosimulation community. BioSimSpace will enable rapid development of workflows between these software packages that can then be used in conjunction with existing workflow software such as Knime, Pipeline Pilot, ExTASY etc. See: https://biosimspace.org 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact BioSimSpace has been used in several CCP-BioSim training workshops, and is now being applied in collaboration with industrialists and experimentalists. 
URL http://www.ccpbiosim.ac.uk
 
Title CCP-BioSim software for biomolecular simulation 
Description BioSimSpace A new software framework to create an interoperability layer around the many software packages that are already embedded within the biosimulation community. BioSimSpace will enable rapid development of workflows between these software packages that can then be used in conjunction with existing workflow software such as Knime, Pipeline Pilot, ExTASY etc. This project is currently in an early phase of development, more information can be found here. FESetup FESetup is a tool to automate the setup of (relative) alchemical free energy simulations like thermodynamic integration (TI) and free energy perturbation (FEP) as well as post-processing methods like MM-PBSA and LIE. FESetup can also be used for general simulation setup ("equilibration") through an abstract MD engine. The latest releases are available from the project web page. Other Software: ProtoMS - a complete protein Monte Carlo free energy simulation package. Sire - a complete python/C++ molecular simulation framework, particularly focussed around Monte Carlo, QM/MM and free energy methods. PCAZIP - a toolkit for compression and analysis of molecular dynamics trajectories. COCO - a tool to enrich an ensemble of structures, obtained e.g. from NMR. Handy Routines for Ptraj/Cpptraj - additional analysis methods for ptraj and cpptraj. 
Type Of Technology Software 
Year Produced 2016 
Open Source License? Yes  
Impact BioSimSpace A new software framework to create an interoperability layer around the many software packages that are already embedded within the biosimulation community. BioSimSpace will enable rapid development of workflows between these software packages that can then be used in conjunction with existing workflow software such as Knime, Pipeline Pilot, ExTASY etc. This project is currently in an early phase of development, more information can be found here. FESetup FESetup is a tool to automate the setup of (relative) alchemical free energy simulations like thermodynamic integration (TI) and free energy perturbation (FEP) as well as post-processing methods like MM-PBSA and LIE. FESetup can also be used for general simulation setup ("equilibration") through an abstract MD engine. The latest releases are available from the project web page. Other Software: ProtoMS - a complete protein Monte Carlo free energy simulation package. Sire - a complete python/C++ molecular simulation framework, particularly focussed around Monte Carlo, QM/MM and free energy methods. PCAZIP - a toolkit for compression and analysis of molecular dynamics trajectories. COCO - a tool to enrich an ensemble of structures, obtained e.g. from NMR. Handy Routines for Ptraj/Cpptraj - additional analysis methods for ptraj and cpptraj. 
URL http://www.ccpbiosim.ac.uk
 
Title CCPBioSim Online Self-guided Training 
Description Tutorials (many based on Jupyter Notebooks) are deployed through containers and accessed through the CCPBioSim website. They cover a range of topics similar to our training events. 
Type Of Technology Webtool/Application 
Year Produced 2019 
Impact The online nature of these tutorials has allowed us to expand our reach and help more people gain computational biology skills. 
URL http://www.ccpbiosim.ac.uk/training
 
Title CCPBioSim Web Portal 
Description A new web portal was launched to replace the old CCPBioSim drupal based website. The new web portal was designed to bring the CCPBioSim web presence in-line with that of HECBioSim. The new portal focuses on providing a collaborative environment where members of the consortium management can create material together that has a consistent and quality look and feel to users, this includes event related materials for conferences and workshops. 
Type Of Technology Webtool/Application 
Year Produced 2016 
Impact Since the launch of the new portal in February 2016, the portal has had around 50,000 hits by 17,847 unique IP addresses indicating that the website has a quite broad reach within the UK bio-simulation community. 
URL http://www.ccpbiosim.ac.uk
 
Title Containerised cloud training platform 
Description The cloud training platform was developed to offer both the HEC and the CCP consortia a new flexible approach to training in the latest and next generation scientific techniques, methodologies and tools. This platform consists of a catalogue of docker containers containing software compiled by our experts, a catalogue of code repositories containing training courses writen by our experts in the JupyterHub/Lab format. This is all brought together in the cloud via kubernetes and results in a platform that researchers and students in our community can simply navigate to our training section on our website and click the course they want to do and the platform will provision a virtual environment with all software and course material ready for them. 
Type Of Technology New/Improved Technique/Technology 
Year Produced 2019 
Impact We have been using this platform to deliver consortia training events in the programme. This has allowed us to deliver thousands of training hours (3,051) across all our courses online and to deliver thousands more (2,510) in instructor led sessions. When the Covid-19 pandemic hit, this infrastructure allowed us to move immediately from events at physical locations to fully online backed by zoom lectures. We even scaled up to having over 400 delegates register with around 200 attending a given session where as we only used to allow around 50 to register and 30 to attend a given session previously with in person classes. 
URL http://www.ccpbiosim.ac.uk/training
 
Title FESetup 
Description FESetup FESetup is a tool to automate the setup of (relative) alchemical free energy simulations like thermodynamic integration (TI) and free energy perturbation (FEP) as well as post-processing methods like MM-PBSA and LIE. FESetup can also be used for general simulation setup ("equilibration") through an abstract MD engine. The latest releases are available from the project web page. 
Type Of Technology Software 
Year Produced 2017 
Impact FESetup FESetup is a tool to automate the setup of (relative) alchemical free energy simulations like thermodynamic integration (TI) and free energy perturbation (FEP) as well as post-processing methods like MM-PBSA and LIE. FESetup can also be used for general simulation setup ("equilibration") through an abstract MD engine. The latest releases are available from the project web page. 
 
Title Longbow v1.5 
Description Longbow is a piece of software that acts as a job proxying tool for biomolecular simulations, Longbow reproduces the native look and feel of using popular molecular dynamics packages (AMBER, CHARMM, GROMACS, LAMMPS and NAMD), with the difference that when those packages are used through Longbow simulations can be run on High Performance Computing (HPC) resources such as ARCHER. Longbow handles jobs setup in terms of creating job submission scripts, automatically stages input files, launches and monitors jobs and stages back simulation results. The option is also there to persistently monitor and stage (realtime local syncing with remote simulation files) simulation files at a specified time interval. This is designed to have the jobs running on the HPC remote resource appear to the user as if the simulation has run on their local computer/cluster. Users do not have to concern themselves with writing submission files, nor do they have to worry about staging. Longbow provides a convenient interface for generating large ensembles of simulation jobs which in effect extends the packages it supports. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact Longbow has now been downloaded 1,523 times from the HECBioSim website and tens of thousands of times from the pypi directory (July 2017). It has a wide reaching user-base across the world, some of those users being at 26 UK institutions actively downloading new versions as they are released. This version was a major new release which focused on addressing a number of architectural problems, this required major refactoring of the code base. This version fixed a number of community reported bugs and added user requested new functionality. Support for the latest python 3 version was added and the API restructured to simplify uptake in other projects. 
URL https://github.com/HECBioSim/Longbow/releases/tag/v1.5.0
 
Title Plug-in and scripts for enhanced-sampling molecular simulations. 
Description We developed a new interoperable plug-in compatible with PLUMED and many widely-used MD codes (such as GROMACS) to run our TS-PPTIS approach for binding kinetics. The tool can be used to predict ligand and folding binding kinetics. 
Type Of Technology Software 
Year Produced 2016 
Open Source License? Yes  
Impact The tool is able to accurately predict the binding kinetics of drugs to their biological targets, paving the avenue to the rational design of new molecules with fine-tuned biomedical effects. 
 
Title ProtoCaller 
Description Software to automate the setup of free energy calculations 
Type Of Technology Software 
Year Produced 2020 
Open Source License? Yes  
Impact non yet 
URL https://protocaller.readthedocs.io/en/latest/index.html
 
Title ProtoMS 3.2 
Description This software allows for the calculation of protein-ligand binding free energies. This most recent version incorporates our latest work on grand canonical Monte Carlo. 
Type Of Technology Software 
Year Produced 2015 
Open Source License? Yes  
Impact This software is being adopted by other academics and some industrial partners are also using it. 
URL http://www.essexgroup.soton.ac.uk/ProtoMS/
 
Title ProtoMS 3.3 
Description This software allows the user to perform protein-ligand binding free energy calculations using advanced Monte Carlo methods, including grand canonical Monte Carlo. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact This software is currently being deployed to industrial collaborators. Its impact in this context will be assessed once these deployments are complete. 
URL http://www.essexgroup.soton.ac.uk/ProtoMS/index.html
 
Title Sire 2014.4 
Description 2014.4 release of Sire. Molecular simulation framework. Main enhancement was the inclusion of new code that accelerated key routines. 
Type Of Technology Software 
Year Produced 2014 
Open Source License? Yes  
Impact Sire is now in use in a number of pharmaceutical companies for applications in drug design and development 
URL http://www.siremol.org/Sire/Home.html
 
Title Software - Crossflow 
Description Crossflow is a Python framework for writing computational workflows for execution on distributed computing facilities. 
Type Of Technology Software 
Year Produced 2020 
Open Source License? Yes  
Impact The software is currently being evaluated by UCB for use in their drug discovery activities 
URL http://bitbucket.org/claughton/crossflow.git
 
Title WaterDock 
Description A software to predict the location of water molecules in proteins. 
Type Of Technology Software 
Year Produced 2016 
Open Source License? Yes  
Impact N/A 
URL https://github.com/bigginlab/WaterDock-2.0
 
Title agnesnoy/SerraLINE: SerraLINE v1.0 
Description Version utilized in the paper: ALB Pyne, A Noy, K Main, V Velasco-Berrelleza, MM Piperakis, LA Mitchenall, FM Cugliandolo, JG Beton, CEM Stevenson, BW Hoogenboom, AD Bates, A Maxwell, SA Harris (2020). "Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and recognition", Accepted in Nat Commun 
Type Of Technology Software 
Year Produced 2020 
Open Source License? Yes  
Impact Publication 
URL https://zenodo.org/record/4105979
 
Title agnesnoy/SerraNA: SerraNA v1.0 
Description By Victor Velasco-Berrelleza and Agnes Noy Published at: V Velasco-Berrelleza, M Burmann, JW Shepherd, MC Leake, R Golestanian, A Noy (2020). "SerraNA: a program to determine nucleic acids elasticity from simulation data" Phys Chem Chem Phys, 22, 19254-19266 https://doi.org/10.1039/D0CP02713H 
Type Of Technology Software 
Year Produced 2020 
Impact Publication and use on subsequent research 
URL https://zenodo.org/record/4105987
 
Title agnesnoy/WrLINE: WrLINEv1.0 
Description By Thana Sutthibutpong and Agnes Noy Published at: Sutthibutpong T, Harris SA, Noy A* (2015). "Comparison of molecular contours for measuring writhe in atomistic supercoiled DNA" J Chem Theor Comput, 11, 2768. DOI:10.1021/acs.jctc.5b00035 
Type Of Technology Software 
Year Produced 2020 
Impact Used in several publications and in current research 
URL https://zenodo.org/record/4106245
 
Company Name VITAMICA LIMITED 
Description Vitamica was established in early 2018 as a spin-out company from the University of Bristol. Taking optical technology from the School of Physics, the new company is beginning its journey towards commercialisation of a rapid and novel diagnostic method that has high potential for use in antimicrobial susceptibility testing. With a growing IP portfolio and an active approach to identifying opportunities in healthcare, veterinary and pharma sectors, Vitamica fully intends to make its mark as another successful company to originate from the University of Bristol. 
Year Established 2018 
Impact The company is working on the development of a rapid AMR diagnostic device that could be used in healthcare, veterinary and pharma sectors.
Website https://www.vitamica.co.uk
 
Description 19th International Union of Pure and Applied Biophysics (IUPAB) and 11th European Biophysical Societies Association (EBSA) Congress in Edinburgh 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Agnes Noy succeed to be selected for giving a talk on the most relevant international conference of the year on Biophysics.
Year(s) Of Engagement Activity 2017
URL http://www.iupab2017.org/home
 
Description 6th Molecular Microbiology Meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact I attended this conference and I gave a talk with the purpose of engaging with microbiologists on multidisciplinary exchange of knowledge
Year(s) Of Engagement Activity 2019
URL https://conferences.ncl.ac.uk/molmicro2019/
 
Description Advanced technology to support research, innovation and economic growth in the UK 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Reform hosted a policy roundtable on the opportunities for advanced technology in the UK in May 2019, with the kind support of Hewlett Packard Enterprise. The session was introduced by Chris Skidmore MP, then Minister of State for Universities, Science, Research and Innovation, and Professor Mark Parsons, Director at the Edinburgh Parallel Computing Centre.

The Minister stressed the importance of international collaboration in R&D, reaffirming the UK's ambition to strengthen and enrich existing
partnerships, as well as to develop new global partnerships - as outlined in the then recently announced International Research & Innovation
Strategy. The discussion also focused on the opportunities the upcoming Comprehensive Spending Review would offer to the science, research and innovation sectors, and on the need to build a strong case for. investment in emerging technologies - including quantum technology, performance computing (HPC) and robotics.

During this meeting it was highlighted that High-performance computing is considered a game-changing technology, which will be fundamental
to the UK's ability to maintain its global competitiveness in the science, research and innovation sectors.
Year(s) Of Engagement Activity 2019
URL https://reform.uk/research/advanced-technology-support-research-innovation-and-economic-growth-uk
 
Description Alchemistry in Boston 2018 - Bluck and Biggin 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A poster was presented on free energy calculations and received useful feedback.
Year(s) Of Engagement Activity 2018
 
Description Article in IFLScience 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Article at the online magazine IFLScience focused in dessmination of scientific news. After 24 hours it had more than 1000 shares
Year(s) Of Engagement Activity 2021
URL https://www.iflscience.com/editors-blog/highestresolution-images-of-dna-ever-reveal-how-it-dances/
 
Description Article in Phys.org 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Article at the Phys.org magazine
Year(s) Of Engagement Activity 2021
URL https://phys.org/news/2021-02-visualization-dna.html
 
Description Article in the Daily Express 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Article in the Daily Express on the article in Nature Communications 2021
Year(s) Of Engagement Activity 2021
URL https://www.express.co.uk/news/science/1398473/dancing-dna-highest-resolution-pictures-dna-molecules...
 
Description Article in the Daily Mail 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Article in the press on the Nature Communications 2021
Year(s) Of Engagement Activity 2021
URL https://www.dailymail.co.uk/sciencetech/article-9265951/Scientists-capture-highest-resolution-images...
 
Description Banff International Research Station for Mathematical Innovation and Discovery: "The Topology of Nucleic Acids" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Invited talk that has been made accessible online
Year(s) Of Engagement Activity 2019
URL https://www.birs.ca/events/2019/5-day-workshops/19w5226
 
Description Biocomputation workshop sponsored by the Physics-of-Life network in Durham 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Agnes Noy participated on the organization of this event in designing the program and selecting the speakers. The event was around the future and scope of biocomputation and how the ideas were articulated for future grants. A grant application was produced as a result of that workshop
Year(s) Of Engagement Activity 2017
URL http://www.physicsoflife.org.uk/biocomputation.html
 
Description Biomolecular Simulations Presentation, DLS, November 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Sarah Fegan gave a presentation on "Biomolecular Simulations" at the Simulations for Experimentalists and Industrialists training course at Diamond Light Source, 7 November 2018. This led to discussions about future research activities.
Year(s) Of Engagement Activity 2018
 
Description Blog and twitter account 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Blog about the scientific research done in my group together with a twiter account @ANoyLab
Year(s) Of Engagement Activity 2019
URL http://agnesnoylab.wordpress.com/
 
Description Bristol Chemshell training Feb 2019 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Tom Keal and You Lu gave a 2-day training course in the use of ChemShell for materials and biomolecular modelling to a group of 15 researchers at the University of Bristol
Year(s) Of Engagement Activity 2019
 
Description CCP5 Summer School, Advanced Lectures in Biomolecular Simulation 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Dr Richard Henchman and Dr Syma Khalid delivered lectures and workshops over three days on how to use simulations study biomolecular systems (setting them up, running them, analysing them). This drew on material given at other CCP-Biosim training events. About 25 student attended from the UK and Europe. The module delivered is one of three given in parallel. Preceding this was the five-day core part of the Summer School.
Year(s) Of Engagement Activity 2015
URL http://www.ccp5.ac.uk/events/summer_school_2015/
 
Description CCPBioSim 2019 annual conference 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact In total, 103 academics, (PhD) students and researchers in industry attended the CCPBioSim conference. The talks and posters presented at the meeting sparked wide-ranging scientific discussions. The feedback was overwhelmingly positive.
(Co-chairs: Marc van der Kamp and Adrian Mulholland)
Year(s) Of Engagement Activity 2019
URL http://www.ccpbiosim.ac.uk/events/past-conferences/eventdetail/119/-/7th-annual-ccpbiosim-conference...
 
Description CCPBioSim Biomolecular QM/MM Modelling with ChemShell workshop, June 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact CCPBioSim held a training day on combined quantum mechanical/molecular mechanical (QM/MM) modelling of biomolecular systems at the University of St Andrews on 14 June 2018 as part of the ScotCHEM 2018 conference. In the morning session we discussed the principles of QM/MM modelling and introduced the ChemShell software package. ChemShell is a scriptable computational chemistry environment which provides a flexible way to link QM and MM codes together to perform QM/MM calculations. There was then an opportunity to learn the basics of ChemShell in the first practical. In the second lecture we described in more depth how QM/MM biomolecular calculations are set up and performed, using a cytochrome P450 system as a case study. The second practical explored modelling of enzymatic reactions with ChemShell on STFC's SCARF cluster.
Year(s) Of Engagement Activity 2018
URL https://www.scotchem.ac.uk/st-andrews-2018/
 
Description CCPBioSim Biomolecular QM/MM Modelling with ChemShell workshop, May 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact CCPBioSim held a training day on combined quantum mechanical/molecular mechanical (QM/MM) modelling of biomolecular systems at STFC Daresbury Laboratory on the 9th May 2017.In the morning session we discussed the principles of QM/MM modelling and introduced the ChemShell software package. ChemShell is a scriptable computational chemistry environment which provides a flexible way to link QM and MM codes together to perform QM/MM calculations. There was then an opportunity to learn the basics of ChemShell in the first practical. In the second lecture we described in more depth how QM/MM biomolecular calculations are set up and performed, using a cytochrome P450 system as a case study. The second practical explored modelling of enzymatic reactions with ChemShell on the Hartree Centre systems. In the final lecture we showcased recent ChemShell developments.
Year(s) Of Engagement Activity 2017
URL http://www.ccpbiosim.ac.uk/events/workshop-course-material/eventdetail/95/-/qm-mm-modelling-of-biomo...
 
Description CCPBioSim Training Week 2018 - QM/MM enzyme reaction modelling 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact During the CCPBioSim training week in 2018, I led a training workshop to introduce non-specialists to the use of combined quantum mechanics/molecular mechanics (QM/MM) methods for modelling enzyme-catalysed reaction mechanisms. I developed new, open-source course material for this, available online. 25 people attended, and evaluated very positively (>60% would strongly recommend the workshop to colleagues, 100% found the workshop (very) useful). Excellent discussion afterwards with several attendees.
Year(s) Of Engagement Activity 2018
URL https://ccpbiosim.github.io/qmmm_workshop/
 
Description CCPBioSim training week, October 2020 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact The CCPBioSim Training Week was held online 2-9 October 2020, organised by Sarah Fegan, Sarah Harris and Charlie Laughton. The topics covered ranged from the basics of biomolecular simulation to QM/MM calculations and there were talks from CCP5 and CCP-EM. There were 17 sessions including three plenary research seminars by Syma Khalid (University of Southampton), Prem Chapagain (Florida International University, USA) and Viv Kendon (Durham University; Chair of CCP-QC). CoSeC representatives James Gebbie, Alin Elena, Michael Seaton and Tom Burnley all gave presentations at the event.
Year(s) Of Engagement Activity 2020
URL https://www.ccpbiosim.ac.uk/events/workshop-course-material/eventdetail/127/-/training-week-2020
 
Description CECAM workshop "Computational biophysics on your desktop: is that possible?" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Invitation of PI grant, Agnes Noy, to give a talk on a CECAM workshop which is a series of scientific conferences
Year(s) Of Engagement Activity 2018
URL https://www.cecam.org/workshop-1534.html
 
Description ChemShell training workshop at PRACE Autumn School 2021: Fundamentals of Biomolecular Simulations and Virtual Drug Development 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A ChemShell biomolecular QM/MM training day was held online as part of the PRACE Autumn School 2021: Fundamentals of Biomolecular Simulations and Virtual Drug Development (20-24 Sep 2021), featuring an introduction to the DL_Software suite by Ilian Todorov, and talks and demonstrations of the ChemShell QM/MM package by Tom Keal, Kakali Sen and You Lu.
Year(s) Of Engagement Activity 2021
URL https://events.prace-ri.eu/event/1222/
 
Description ChemShell training workshop at the CCPBioSim training week, September 2021 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact As part of the CCPBioSim training week 2021, a training session on ChemShell for biomolecular QM/MM calculations was held, with talks and demonstrations from Tom Keal, Kakali Sen, You Lu and Sarah Fegan of STFC.
Year(s) Of Engagement Activity 2021
URL https://www.ccpbiosim.ac.uk/events/workshop-course-material/eventdetail/135/-/ccpbiosim-training-wee...
 
Description Conference paper at Physics in Food manufacturing event, Chipping Campden, January 2019. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Workshop organised by the Institute of Physics food group. Allowed networking with physicists/physical chemists with similar intersts in food science.
Year(s) Of Engagement Activity 2019
 
Description Conference paper on Food Oleogels at EFFost conference November 2018 in Nantes France 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Discussion were held with industrial (and academic) scientists who were interested in the finding of the work.The computational approaches used were of particular interests to academics and this has fostered new interactions with potential academic collaborators.
Year(s) Of Engagement Activity 2018
 
Description EUTOPIA-2: 2 nd meeting of the European Topology interdisciplinary Initiative 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Invited talk and enroll at this EU-funded COST network
Year(s) Of Engagement Activity 2019
URL https://eutopiaam2019.wordpress.com
 
Description HECBioSim: tools to simplify running and analysing large-scale MD simulations on HPC resources 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact This workshop was to introduce members of the bio-simulation community to tools that simplify the process of running and analysing MD simulations on a large scale. Users were introduced to consortia developed tools (Longbow pyPcazip and pyPcazipgui), users attempted hands on demonstrations of how to use such software and how to introduce them into their own workflows. Users had access to the national super computing service ARCHER for the duration of this workshop, so they had hands on experience with such resources for the first time in some cases.

This workshop provided users direct exposure to the developers of the tools, which helped to open dialogue between users and developers and bring more ideas for new features.
Year(s) Of Engagement Activity 2015
URL http://www.ccpbiosim.ac.uk/hecbio-goinglarge
 
Description Headstart program at the University of York 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Supporters
Results and Impact Guest lecture "Introduction to Biophysics" to A-level physics students within the Work Experience Week and Headstart programs
Year(s) Of Engagement Activity 2019
URL https://www.york.ac.uk/physics/public-and-schools/events/headstart-2019/
 
Description Industry training workshops 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Training on our software ProtoMS was given to three industrial partners - GSK, AZ and UCB. This involved visits to the industrial sites, presentation of the theory underpinning the work, and the provision of training materials.
Year(s) Of Engagement Activity 2017
 
Description Interview in That's York TV 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Interview for the local TV
Year(s) Of Engagement Activity 2021
URL https://www.facebook.com/ThatsTVYork/
 
Description Istanbul December 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A talk on free energy.
Year(s) Of Engagement Activity 2018
 
Description Joint CCP-BioSim CCP-EM workshop on Computation for cryo-EM 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact The first day of the workshop provided new users of the Fluctuating Finite Element analysis software (developed at Leeds). As this is the first time this software has been used by people outside of the group, we obtained very useful feedback on performance and usability. The software has been adopted by at least one other research team since the event. On the second day, we had the first (to our knowledge) community discussion of the role of computation in cryo-EM from a prestigious range of international speakers. The event was extremely well received, and we are planning a subsequent workshop for 2019.
Year(s) Of Engagement Activity 2017
 
Description London Free Energy Meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I presented a talk on free energy calculations to specialised audience of practitioners including industry attendees.
Year(s) Of Engagement Activity 2017
 
Description Lorentz-Center workshop on DNA Damage and Repair in Leiden, Netherlands 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Agnes Noy was invited to give a talk and to participate as an expert panel on a dialogue about the subject with numerous questions and long discussions
Year(s) Of Engagement Activity 2017
URL http://www.lorentzcenter.nl/lc/web/2017/932/info.php3?wsid=932&venue=Oort
 
Description Markov modelling and free energy calculation workshop 2016 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact About 50 participants attended the Markov modelling workshop we organised at King's College London, some of which were international scientists from India, Europe or the US. Several participants were from pharmaceutical companies, such as Novartis, GSK, and UCB Pharma. The workshop initiated further collaborations and research visits with both academic groups and pharma companies.
Year(s) Of Engagement Activity 2016
 
Description Multiscale Modelling Conference jointly between CCPBiosim and CCP5 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Conference of 100 people bringing together experts in the UK, Europe and USA in the area of multiscale modelling in a 2-day conference in Manchester in April 2016. There are about 30 talks and a poster session of about 40 posters. The conference ran previously in January 2014 with a similar size and format.
Year(s) Of Engagement Activity 2014,2016
URL http://www.ccpbiosim.ac.uk/multiscale2016/eventdetail/55/-/2nd-conference-on-multiscale-modelling-of...
 
Description Multiscale modelling presentation, DLS, November 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Tom Keal gave a presentation on "Multiscale modelling of biomolecules and materials" at the Simulations for Experimentalists and Industrialists training course at Diamond Light Source, 7 November 2018
Year(s) Of Engagement Activity 2018
 
Description Pint of Science 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Outreach talk for general public about current research in genomes and how affects our lives.
Year(s) Of Engagement Activity 2019
URL https://pintofscience.co.uk/
 
Description Pint of Science talk: Making movies of Bacterial membranes 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact I gave a talk in a pub to an audience consisting of members of the general public who had bought tickets to the event. The talk explained some of the science behind antimicrobial resistance followed by some details of my own work in terms of 'making movies' of the bacterial membranes so we can understand how they protect bacteria. I talked about how we have to understand the membranes in molecular detail if we are to design new drugs with the ability to permeate across these membranes. Audience members said they had a much better understanding of how they must not abuse antibiotics, after the talk.
Year(s) Of Engagement Activity 2017
URL https://pintofscience.co.uk/event/architecture-with-atoms
 
Description Press release by the University of York 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact Press Release on the article on Nature Communications 2021
Year(s) Of Engagement Activity 2021
URL https://www.york.ac.uk/news-and-events/news/2021/research/dna-dancing-video/
 
Description Seminar at University of Leeds 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact Seminar on edible oleogels at the University of Leeds to academic staff and students
Year(s) Of Engagement Activity 2017
 
Description Special Seminar on Entropy 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Richard Henchman gave a talk about his multiscale cell correlation technique for calculating and analysing entropy from simulation data. The talk was followed by 30 minutes of answering questions from the audience. Abstract: The stability and flexibility of biomolecules are inherent to their properties and function. Entropy is central to both these quantities, first because it is a key component of the free energy, which governs stability, and second because it expresses the probability distribution over all degrees of freedom in a single number. While there are methods to evaluate entropy for specific cases and while there are many partial measures of molecular
flexibility, a general way to evaluate the entropy and full probability distribution is lacking for systems of biomolecular interest. To address this, we present the Multiscale Cell Correlation (MCC) method [1-2] which calculates entropy in a multiscale fashion in terms of cells of correlated units. We apply it to two cases: host-guest complexes [3] and proteins [4]. Binding free energies in the recent SAMP8 Challenge give a 1 kcal mol-1 error, and protein entropies closely match values from normal mode analysis. MCC explains how entropy is distributed over all degrees of freedom in each system. For binding, as expected, the entropy loss of the binding guest is offset by the gain in the released water. In proteins, entropy in the polymer chain is found to be comparable to that within the residues, and the residue entropy is largely independent of solvent exposure due to a compensation between conformational and vibrational entropy.
[1] J. Higham, S. Chou, F. Gräter, R. H. Henchman, Mol. Phys., 2018, 116, 1965.
[2] H. S. Ali, J. Higham, R. H. Henchman, Entropy, 2020, 21, 750.
[3] H. S. Ali, A. Chakravorty, J. Kalayan, S. P. de Visser, R. H. Henchman, submitted.
[4] A. Chakravorty, J. Higham, R. H. Henchman, J. Chem. Inf. Model., 2020, 60, 5540.
Year(s) Of Engagement Activity 2021
URL http://www.ccpbiosim.ac.uk/entropy2021
 
Description Sweden Keynote Presentation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I gave a keynote presentation on drug design to a specialist audience.
Year(s) Of Engagement Activity 2018
 
Description Talk at Bristol Scientific Club 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Other audiences
Results and Impact I gave a presentation which covered the use of holographic tweezers to control 3D-printed micro tools as a 3D optical AFM. The audience was from a wide science and engineering background and I believe the talk was received with enthusiasm. One result was that I was invited to join this prestigious club.
Year(s) Of Engagement Activity 2017
 
Description Talk give in Oxford to Shanghai Tech 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact A talk was given on free energy calculations as part of a discussion to investigate joint operations between the university and Shanghai Tech.
Year(s) Of Engagement Activity 2018
 
Description Talk in Dundee 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact A talk to 50-60 scientists from the Dundee area that provoked some interesting ideas and discussion.
Year(s) Of Engagement Activity 2017
 
Description Talk in the Physics of Life - Physics of Medicine Network Launch Event 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Launch event of the third network of Physics of Life funded by the three UKRI councils EPSRC, MRC, BBSRC, Rosetrees Trust and the Universities of York, Durham and Leeds
Year(s) Of Engagement Activity 2020
URL http://www.physicsoflife.org.uk
 
Description Talk on "Why is life so complicated, can my computer help"? at Edinburgh science festival 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Talk at Edinburgh science festival explaining how supercomputing helps us to understand molecular biology.
Year(s) Of Engagement Activity 2017
 
Description Talk on "Why supercomputing is like Christmas" for the Wanstrow Christmas Lectures 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact I explain how supercomputers are used to help scientists at the annual Wanstrow Christmas Lectures, Wanstrow Village Hall, Somerset.
Year(s) Of Engagement Activity 2017
 
Description Training workshop on using TINKER with the AMOEBA force field 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact We arranged a one-day training workshop on using the AMOEBA force field in the context of the TINKER molecular dynamics software.
Year(s) Of Engagement Activity 2016
URL https://sites.google.com/site/amoebaworkshop/
 
Description UKQSAR Sept 2018 Meeting - Bromodomains and Drug design 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A talk on drug design given.
Year(s) Of Engagement Activity 2018
 
Description Vertex 2018 Talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact An invited talk given to Vertex Pharmaceuticals.
Year(s) Of Engagement Activity 2018
 
Description Yale iGluR Poster Presentation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Poster presentation to about 130 scientists in the field of glutamate research
Year(s) Of Engagement Activity 2017
 
Description YouTube Channel 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Recordings of CCPBioSim organised talks and training are shared on the YouTube Channel (with the speaker's permission). This allows anyone who missed the event or would like to review the material again to watch the video at any convenient time. We hope that this makes computational biology more accessable.
Year(s) Of Engagement Activity 2020,2021
URL https://www.youtube.com/channel/UCJLWsk2Hbhf09--POlR67Nw