The UK High-End Computing Consortium for Biomolecular Simulation
Lead Research Organisation:
University of Southampton
Department Name: Sch of Chemistry
Abstract
There is tremendous future scope for biomolecular simulation to provide unprecedented insights into biomolecular systems. The level of detail afforded by these methods, along with their ability to rationalise experimental data and their predictive power are already enabling them to make significant contributions in a wide variety of areas that are crucial for healthcare, quality of life and the environment. The UK biomolecular simulation community has a strong international reputation, with world-leading efforts in in drug design and development, biocatalysis, bionano-technology, chemical biology and medicine. HECBioSim has already delivered outstanding research with impact in bionanotechology, drug design and AMR. But we have only just scratched the surface and there is currently huge room for expansion. Having access to the largest, most modern computing facilities is essential for this. Renewal of the Consortium will enable us to continue allocating time ARCHER for cutting-edge biomolecular simulations.
We will place a special emphasis on reaching out to experimentalists and scientists working in industry in order to foster interactions between computational and experimental scientists, and academia and industry to encourage integrated multidisciplinary studies of key problems.
Biomolecular simulation and modelling is an integral part of drug design and development. The pharmaceutical industry needs well-trained scientists in this area, as well as the development of new methods (e.g. for prediction of drug binding affinities, ligand selectivity and metabolism). Members of the consortium have a strong track record of collaboration with industry to deliver trained scientists and new methodologies. For example, PhD students trained by consortium members have recently taken up positions in UCB, Unilever, Oxford Nanoimaging and even Sky Broadcasting as software developer. Many of these academic-industry collaborations have been strengthened by work done through HECBioSim allocations.
The Consortium will continue to welcome new members from across the whole community. We will continue to develop computational tools and training for both experts and non-experts using biomolecular simulation on HEC resources. We propose to develop new tools that will enable inter-conversion between biomolecular systems at different levels of resolution thereby allowing users to tackle more ambitious 'grand challenges' than are currently feasible.
In summary HECBioSim will foster collaborations between computational and experimental scientists between scientists working in industry and academia in all disciplines within biomolecular simulation to maintain the UK as a world-leader in this field.
We will place a special emphasis on reaching out to experimentalists and scientists working in industry in order to foster interactions between computational and experimental scientists, and academia and industry to encourage integrated multidisciplinary studies of key problems.
Biomolecular simulation and modelling is an integral part of drug design and development. The pharmaceutical industry needs well-trained scientists in this area, as well as the development of new methods (e.g. for prediction of drug binding affinities, ligand selectivity and metabolism). Members of the consortium have a strong track record of collaboration with industry to deliver trained scientists and new methodologies. For example, PhD students trained by consortium members have recently taken up positions in UCB, Unilever, Oxford Nanoimaging and even Sky Broadcasting as software developer. Many of these academic-industry collaborations have been strengthened by work done through HECBioSim allocations.
The Consortium will continue to welcome new members from across the whole community. We will continue to develop computational tools and training for both experts and non-experts using biomolecular simulation on HEC resources. We propose to develop new tools that will enable inter-conversion between biomolecular systems at different levels of resolution thereby allowing users to tackle more ambitious 'grand challenges' than are currently feasible.
In summary HECBioSim will foster collaborations between computational and experimental scientists between scientists working in industry and academia in all disciplines within biomolecular simulation to maintain the UK as a world-leader in this field.
Planned Impact
Who might benefit from this research?
The direct beneficiaries of this research include academic and industrial scientists, including experimentalists working across a very wide range of disciplines including X-ray crystallography, NMR, electron microscopy, single molecule biophysics methods, mass spectrometry, hydrodynamics, enzyme kinetics, drug design medicinal chemistry, chemical and synthetic biology and design on biosensors. The two most obvious industrial beneficiaries are the pharmaceutical sector, which is of huge economic importance to the UK; and the biotechnology sector in which the UK is a world leader in e.g. nanopore DNA sequencing. Other industries (such as biocatalysis analysis and processing, IT hardware and software development) will also benefit from the UK High-End Computing Consortium for Biomolecular Simulation (HECBioSim) through our already established excellent links and new ones that will be fostered through the renewal of the Consortium. In the longer term, All of the work will impact on the general public through improvements in health and quality of life.
How will they benefit?
The focus of HECBioSim is to support access and use of high-end computing in the UK, both in terms of increased uptake and awareness by experimental colleagues, but also from experimental groups in both academia and industry. We also engage other interested parties and the general public.
Focused Training workshops and webinars:
We will undertake 3-4 workshops that will have a definitive focus on engaging more strongly with: i) industrial users, ii) experimental groups (mainly in academia but could also be from industry) and iii) emerging technology areas (including cryo-EM, and machine learning). We propose to deliver an annual webinar, showcasing HECBioSim outputs. Webinars offer the distinct advantage that they are virtual and can be accessed by anyone worldwide for zero cost to participants.
Making it easier for industry and academics to adopt.
In industry the use of electronic notebooks is widespread and the capture of metadata for experiments and simulations is absolutely critical. In order to make the use and adoption of HPC simulation data more viable, we plan to develop quality control metrics for simulation data and integrate capturing this information seamlessly into electronic notebooks. These electronic notebooks will be of benefit for industrial and academic scientists and will facilitate multidisciplinary projects.
Engagement to a more general audience.
We propose to put in a proposal for major science festivals including the Summer Science Exhibition at the Royal Society or the Cheltenham Science Festival to reach out to the wider community. Furthermore we will also generate a short promotional video that highlights the role of the HECBioSim and the impact that the work it supports has on UK science and the benefit to the general public. This will be hosted on our main website but we will disseminate via as many other routes as well (for example, youtube). We will highlight key results from the consortium via the website but also via social media, mainly via Twitter.
Maximizing code development potential
We plan to continue to develop our existing codes, which are already freely available Longbow and FESetup in addition to a new project which will focus around providing an easy-to-use interface for running coarse-grain and atomistic simulations and quantum mechanics calculations and interconverting between them, on HEC resources. This will be provided free of charge to the academic community along with training material.
Commitment to Diversity
We are committed to a philosophy of diversity within our science. To ensure this, we have made contact with Women in high Performance Computing ), in order to work closely with them to ensure a fair gender representation across all of our activities.
The direct beneficiaries of this research include academic and industrial scientists, including experimentalists working across a very wide range of disciplines including X-ray crystallography, NMR, electron microscopy, single molecule biophysics methods, mass spectrometry, hydrodynamics, enzyme kinetics, drug design medicinal chemistry, chemical and synthetic biology and design on biosensors. The two most obvious industrial beneficiaries are the pharmaceutical sector, which is of huge economic importance to the UK; and the biotechnology sector in which the UK is a world leader in e.g. nanopore DNA sequencing. Other industries (such as biocatalysis analysis and processing, IT hardware and software development) will also benefit from the UK High-End Computing Consortium for Biomolecular Simulation (HECBioSim) through our already established excellent links and new ones that will be fostered through the renewal of the Consortium. In the longer term, All of the work will impact on the general public through improvements in health and quality of life.
How will they benefit?
The focus of HECBioSim is to support access and use of high-end computing in the UK, both in terms of increased uptake and awareness by experimental colleagues, but also from experimental groups in both academia and industry. We also engage other interested parties and the general public.
Focused Training workshops and webinars:
We will undertake 3-4 workshops that will have a definitive focus on engaging more strongly with: i) industrial users, ii) experimental groups (mainly in academia but could also be from industry) and iii) emerging technology areas (including cryo-EM, and machine learning). We propose to deliver an annual webinar, showcasing HECBioSim outputs. Webinars offer the distinct advantage that they are virtual and can be accessed by anyone worldwide for zero cost to participants.
Making it easier for industry and academics to adopt.
In industry the use of electronic notebooks is widespread and the capture of metadata for experiments and simulations is absolutely critical. In order to make the use and adoption of HPC simulation data more viable, we plan to develop quality control metrics for simulation data and integrate capturing this information seamlessly into electronic notebooks. These electronic notebooks will be of benefit for industrial and academic scientists and will facilitate multidisciplinary projects.
Engagement to a more general audience.
We propose to put in a proposal for major science festivals including the Summer Science Exhibition at the Royal Society or the Cheltenham Science Festival to reach out to the wider community. Furthermore we will also generate a short promotional video that highlights the role of the HECBioSim and the impact that the work it supports has on UK science and the benefit to the general public. This will be hosted on our main website but we will disseminate via as many other routes as well (for example, youtube). We will highlight key results from the consortium via the website but also via social media, mainly via Twitter.
Maximizing code development potential
We plan to continue to develop our existing codes, which are already freely available Longbow and FESetup in addition to a new project which will focus around providing an easy-to-use interface for running coarse-grain and atomistic simulations and quantum mechanics calculations and interconverting between them, on HEC resources. This will be provided free of charge to the academic community along with training material.
Commitment to Diversity
We are committed to a philosophy of diversity within our science. To ensure this, we have made contact with Women in high Performance Computing ), in order to work closely with them to ensure a fair gender representation across all of our activities.
Organisations
- University of Southampton (Lead Research Organisation)
- Complutense University of Madrid (Collaboration)
- Columbia University (Collaboration)
- European Cooperation in Science and Technology (COST) (Collaboration)
- University of Virginia (UVa) (Collaboration)
- Case Western Reserve University (Collaboration)
- UCB Pharma (Collaboration)
- Trinity College Dublin (Collaboration)
- UNIVERSITY OF OXFORD (Collaboration)
- Henry Royce Institute (Collaboration)
- University of Sheffield (Collaboration)
- John Innes Centre (Collaboration)
- Medical Research Council (MRC) (Collaboration)
- AstraZeneca (United Kingdom) (Project Partner)
- Vernalis plc (Project Partner)
- UCB Pharma (Belgium) (Project Partner)
Publications
Abraham M
(2019)
Sharing Data from Molecular Simulations
Abraham M
(2019)
Sharing Data from Molecular Simulations
in Journal of Chemical Information and Modeling
Ali HS
(2019)
Entropy of Simulated Liquids Using Multiscale Cell Correlation.
in Entropy (Basel, Switzerland)
Alibay I
(2022)
Evaluating the use of absolute binding free energy in the fragment optimisation process
in Communications Chemistry
Amaro RE
(2020)
Biomolecular Simulations in the Time of COVID19, and After.
in Computing in science & engineering
Amaro RE
(2020)
A Community Letter Regarding Sharing Biomolecular Simulation Data for COVID-19.
in Journal of chemical information and modeling
Amos STA
(2021)
Membrane Interactions of a-Synuclein Revealed by Multiscale Molecular Dynamics Simulations, Markov State Models, and NMR.
in The journal of physical chemistry. B
| Description | Collaboration of Khalid with Rommie Amaro (UCSD, USA) and Michael Feig (Michigan, USA) New collaboration initiated in April 2020 to model the M protein of the SARS-Cov2 virus. The structure of this protein (the most abundant protein in the viral membrane) is not known yet it is essential for the structural integrity of the viral particle. Khalid, Amaro and Feig are using bioinformatics, molecular modelling and multiscale simulations to predict the structure of the protein and its arrangement within the viral membrane including around the spike protein. The coarse-grained simulations are being run on Archer while the atomistic simulations are being run on Frontera at the Texas Advanced Supercomputer Center. A manuscript is in preparation. The collaboration of Khalid with Amaro's team and other US teams resulted in the award of the Gordon-Bell Special Prize for Covid19 related work. This made mainstream news in the USA. A preprint is available here: doi: https://doi.org/10.1101/2020.11.19.390187 Collaboration of Khalid with Wonpil Im (Lehigh, USA) Khalid has been collaborating with Wonpil Im (Lehigh, USA) to use the hydrogen mass repartitioning technique to enable faster simulations of bacterial membranes. The preprint was uploaded during the reporting period but the paper came out just after so will be included in the next annual report. This work represents an important advancement as it enables users on ARCHER to use longer time steps with the CHARMM force-field thereby speeding up simulations. We expect this study to be highly cited given its methodological utility and that the time-step can be set-up via the free online server CHARMMGUI Collaboration of Khalid with Gizela Storz (NIH, USA) This is a collaboration that is also involves Ben Luisi (Cambridge) and brings together multiple experimental methods with computer simulations to understand protein-protein and protein-lipid interactions in a bacterial membrane environment. • Du D, Neuberger A, Orr MW, Newman CE, Hsu PC, Samsudin F, Szewczak-Harris A, Ramos LM, Debela M, Khalid S, Storz G, Luisi BF (2020), Interactions of a Bacterial RND Transporter with a Transmembrane Small Protein in a Lipid Environment. Structure Collaboration of Sansom with Sudha Chakrapani, (Case Western U, Cleveland, USA), ARCHER allocations through HECBioSim were used for a number of joint studies of ion channel structure function relationships with both collaborators leading to the following publications: • Kumar, A., Basak, S., Rao, S., Gicheru, Y., Mayer, M.L., Sansom, M.S.P. & Chakrapani, S. (2020) Mechanisms of activation and desensitization of full-length glycine receptor in membranes. Nature Communicatons. Collaboration of Sansom, Kalli and Stansfeld with Eiji Yamamoto (Keio University, Japan) and Robert Best (NIH, USA). Further details are in one of our case studies. • Yamamoto E, Domanski J, Naughton FB, Best RB, Kalli AC, Stansfeld PJ, Sansom MSP. (2020) Multiple lipid binding sites determine the affinity of PH domains for phosphoinositide-containing membranes, Science Advances Collaboration of Sansom with David Baker (University of Washington, USA) This is a newly established collaboration in which the combined expertise of the UK and USA groups are being used for de novo design of membrane protein pores. A PhD student (Shanlin Rao) from the Sansom group is being trained as part of the project, which from the UK side relies on HPC provided via HECBioSim. Stansfeld: multiple international collaborations: Jochen Zimmer (Virginia, US) Linda Columbus (Virginia, US) Inga Hanelt (Frankfurt, Germany) • Structural basis of the proton-coupled potassium transport in the KUP family Igor Tascón, Joana Sousa, Robin Corey, Deryck Mills, David Griwatz, Nadine Aumüller, Vedrana Mikusevic, Phillip J. Stansfeld, Janet Vonck, Inga Hanelt, Nature Communications Cristina Paulino (Groningen, Netherlands) John Parkinson (Utah, US) Irina Gutsche (Grenoble, France) • Complete structure of the core signalling unit of the E. coli chemosensory array in an optimised minicell strain. Alister Burt, CK Cassidy, Peter Ames, Maria Bacia-Verloop, Megghane Baulard, Karine Huard, Zaida Luthey-Schulten, Ambroise Desfosses, Phillip J. Stansfeld, William Margolin, John Parkinson, Irina Gutsche. Nature Communications, 2020 Filippo Mancia (Columbia, US) Jonathan Dworkin (Columbia, US) Ed Yu (Case Western, US) Multiple international authors from UK, Slovenia, USA • Structure and mechanism of bactericidal mammalian perforin-2, an ancient agent of innate immunity, Tao Ni, Fang Jiao, Xiulian Yu, Saša Aden, Lucy Ginger, Sophie Williams, Fangfang Bai, Vojtech Pražák, Dimple Karia, Phillip Stansfeld, Peijun Zhang, George Munson, Gregor Anderluh, Simon Scheuring, Robert J. C. Gilbert, Science Advances, 2020 Gervasio with Karl-Heinz Krause (Geneva): Collaboration with Prof. Karl-Heinz Krause, faculty of Medicine University of Geneva. Understanding the effect of Mutations in SARS-CoV2 Spike protein. Preprint available at https://www.medrxiv.org/content/10.1101/2020.08.23.20180281v1, submitted for publication). Mulholland with Amaro (UCSD) • Biomolecular simulations for covid applications, highlighting HECBioSim activity, are reviewed in: 'Biomolecular Simulations in the Time of COVID-19, and After' R.E. Amaro and A.J. Mulholland Computing in Science & Engineering Nov.-Dec. 2020, pp. 30-36, vol. 22 DOI: 10.1109/MCSE.2020.3024155 • COVID19 - Computational Chemists Meet the Moment, Adrian J. Mulholland and Rommie E. Amaro J. Chem. Inf. Model. 2020. • Simulations support the interaction of the SARS-CoV-2 spike protein with nicotinic acetylcholine receptors A. Sofia F. Oliveira, Amaurys Avila Ibarra, Isabel Bermudez, Lorenzo Casalino, ZiedGaieb, Deborah K. Shoemark, Timothy Gallagher, Richard B. Sessions, Rommie E. Amaro, Adrian J. Mulholland https://www.biorxiv.org/content/10.1101/2020.07.16.206680v3 Mulholland with multiple international authors: • Free fatty acid binding pocket in the locked structure of SARS-CoV-2 spike protein Science 370 725-730 (2020) https://science.sciencemag.org/content/370/6517/725 Additional time has been provided where needed leading to some large, and important collaborations, for example Vendruscolo is working with the Rosalind Franklin Institute to study the dynamics of antibodies that bind the viral spike protein (a follow on of the project described here: https://www.rfi.ac.uk/engineered-llama-antibodies-neutralise-covid-19-virus/). Both Vendruscolo and Mulholland are currently using time on Bede and ARCHER2 respectively allocated via evaluation by HECBioSim to study the newly emerged mutations in the spike protein (UK and South Africa strains). New industrial and overseas collaborations have been established in which simulations performed on ARCHER are facilitating the development of anti-virals that target the SARS-CoV2 virus. These include: • Gervasio (UCL): collaboration with Mone Zaidi, Mount Sinai School of Medicine and DeepMind - London (Designing therapeutic peptides for COVID). • Biggin (Oxford): collaboration with IBM on designing antivirals targeting SARS-CoV2 enzymes. • Mulholland (Bristol) collaboration with: Geneva Biotech Sàrl and Imophoron Ltd to characterise druggable sites on the SARS-CoV2 Spike protein. |
| Exploitation Route | Our work has resulted in new insights into how and where molecules may bind to SARS-Cov2 proteins which can be used by others to: Develop drugs Look allosteric effects of mutations We have uncovered many details of protein-lipid interactions (see publications) which can be used by those working on imaging membrane proteins to help interpret their imaging data. We have provided design principles of nanopores which are advantageous for applications in bionanotechnology which can be used by others to translate into new pores or to help understand microscopic behaviour of existing pores. |
| Sectors | Chemicals Healthcare Pharmaceuticals and Medical Biotechnology |
| URL | https://doi.org/10.1016/j.jmb.2020.01.008 |
| Description | Sansom (Oxford): UCB have supported a number of BBSRC iCASE studentships in the general area of membrane protein/lipid interactions, all of which have benefitted from ARCHER access. These molecular interactions play a key role in modulating the function of membrane proteins implicated in many diseases, and therefore are of importance to pharmaceutical companies such as UCB. Sansom (Oxford) and Stansfeld (Warwick): IBM support an EPSRC iCASE studentship to examine peptide /lipid interactions which also benefits from ARCHER access. This has resulted in a preprint within the funding period: (which is now published, but just after this reporting period): Biggin (Oxford) We have been extending our work on absolute binding free energies to fragment design with Boehringer Ingelheim, via a fully-funded PDRA. New code has been developed as part of this collaboration, which will be made available soon. An iCASE studentship on membrane proteins is funded by Vertex. Both projects have been built on the successful usage of ARCHER via HECBioSim. Khalid (Oxford) A studentship funded through Oxford Nanopore Technologies Ltd (ONT) relies upon access to ARCHER via HECBioSim. We are simulating the protein used in the commercial devices made by the world leading nanopore DNA sequencing company. Much of the work cannot be published due to the highly sensitive nature of the details of the engineered protein being used. However a paper on a model system has been published as well as second on the wildtype protein complex CsgG/F with the Steve Matthews and Sarah Rouse groups at Imperial College (also HECBioSim members). Discussion is ongoing with ONT for future funding. Essex (Southampton) A PhD student has been exploring the conformations of the recognition loops of antibodies to understand how they achieve such high affinity and specificity. This work is supported by UCB Another PhD student is using ARCHER2 to simulate the protein complex apoferritin in very large volumes of water, to provide model data to explore the accuracy of cryo-EM image reconstruction algorithms. This is in collaboration with the Rosalind Franklin Institute. Publications from both of these projects are in the pipeline. Michel (Edinburgh) PhD student funded by Cresset. The Michel group and Cresset are using HPC provided through HECBioSim to develop machine-learned (ML) models of the difficulty of protein ligand binding Free Energy Perturbation (FEP) calculations. The ML models are used to power new automated FEP workflows for high-throughput studies that support industrial drug design R&D efforts. Fraternali (King's College London). A novel antimicrobial nanocapsule construct able of self assembly. The results are presented in the manuscript under revision "Nanocapsule Designs for Antimicrobial Resistance". The project carried on previous work performed in collaboration with the National Physics Laboratory (UK), and prompted a collaboration with Unilever (UK) for the investigation of analogous antimicrobial peptides interactions and self-assembly. Unilever provided funding for a PDRA, access to ARCHER via HECBioSim played a role in securing the funding and setting up the collaboration. Such molecules are of interest for the company, aiming at incorporating antimicrobial elements into its products. Two manuscripts are resulting from this collaboration, one is in second revision and the other is in preparation. Stansfeld (Warwick) PhD studentship funded by OMASS has yielded the paper: Ligand induced conformational dynamics of the LPS translocon LptDE. Francesco Fiorentino, Joshua B. Sauer, Xing Yu Qiu, Robin A. Corey, C. Keith Cassidy, Benjamin Mynors-Wallis, Shahid Mehmood, Jani Reddy Bolla, Phillip J. Stansfeld, Carol V. Robinson (2020) Nature Chemical Biology. The simulations reported here were performed on ARCHER with access provided by HECBioSim Gervasio (UCL) Collaboration with Ben Cossins (UCB, Slough) on developing accurate algorithms for ligand binding free energy calculations Collaboration with Astra Zeneca (who are co-sponsoring an industrial student with EPSRC): understating the effects of cancer-causing mutations on the structure and dynamics of EGFR. |
| Sector | Chemicals,Healthcare,Pharmaceuticals and Medical Biotechnology |
| Impact Types | Societal |
| Description | Invited contribution to DiRAC workshop on future UKRI Digital Research Infrastructure. |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Description | Presentation to HPC-AI Advisory Council |
| Geographic Reach | Multiple continents/international |
| 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 | participation at digital research infrastructure meeting |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| 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 | 09/2019 |
| End | 09/2022 |
| 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 | 09/2017 |
| End | 09/2020 |
| 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 | Oracle for Research Cloud Fellowship |
| Amount | $100,000 (USD) |
| Organisation | Oracle Corporation |
| Sector | Private |
| Country | United States |
| Start | 02/2023 |
| End | 12/2023 |
| 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 | 09/2021 |
| End | 09/2026 |
| Description | UKRI CoA Extension |
| Amount | £24,675 (GBP) |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2020 |
| 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 | 08/2022 |
| End | 09/2022 |
| 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 |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2006 |
| End | 02/2033 |
| 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 |
| 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 |
| URL | https://springernature.figshare.com/articles/dataset/Atomic_force_microscopy_and_atomistic_molecular... |
| Title | Cyclic di-AMP traps proton-coupled K+ transporters of the KUP family in an inward-occluded conformation |
| Description | Raw data of whole-cell K+ transport data and DSF measurements, detailed information provided in the according paper |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Cyclic_di-AMP_traps_proton-coupled_K_sup_sup_tr... |
| Title | Cyclic di-AMP traps proton-coupled K+ transporters of the KUP family in an inward-occluded conformation |
| Description | Raw data of whole-cell K+ transport data and DSF measurements, detailed information provided in the according paper |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Cyclic_di-AMP_traps_proton-coupled_K_sup_sup_tr... |
| Title | Dataset for CDL vs MLCL in mitochondrial Complex III - Complex IV supercomplexes |
| Description | Coarse-grained structure (gro) and trajectory (xtc) files for yeast, mouse, and human respiratory supercomplexes in a membrane containing either cardiolipin (CL) or monolysocardiolipin (MLCL). Atomistic structure (gro) and trajectory (xtc) files for the yeast respiratory supercomplex in a membrane containing either CL or MLCL. Three repeats of each simulation are present in each case. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | https://zenodo.org/record/7261107 |
| Title | Experimental and molecular modelling data from the study of 46mer DNAzyme |
| Description | Here we are providing access to experimental and molecular dynamics (MD) simulation data from the study of 46mer DNAzyme. Experimental data: NMR experiments for the determination of the diffusion coefficients of the c4, s4, c4s4 without and with Copper(II). (NMR.zip) EPR/ESR experiments, both 1D and 2D, for the determination of g-factors and hyperfine couplings with Cu2+ Mass spectroscopy for the analysis of DNA fragments before and after the cleavage reactions Molecular dynamics data: Atomic pdb models of 46mer DNAzyme with (46m_WithCU.pdb) and without Cu2+ ions (46m_WithoutCU.pdb) Ten trajectories/replicas of 46mer DNAzyme with Cu2+ ions (1-10 46m-WithCU-500ns_dt100ps.xtc) Three trajectories/replicas of 46mer DNAzyme without Cu2+ ions (1-3 46m-WithoutCU-500ns_dt100ps.xtc) Each replica contains 500 nanaoseconds of simulation data sampled at 100 picosecond intervals. Simulations were done using GROMACS2020 package using parmbsc1 forcefield on JADE2 cluster. This project made use of time on HPC granted via the UK High-End Computing Consortium for Biomolecular Simulation, HECBioSim (http://hecbiosim.ac.uk), supported by EPSRC (grant no. EP/R029407/1). EPR experiments were supported by financial support from the IR INFRANALYTICS FR2054. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| URL | https://brunel.figshare.com/articles/dataset/Experimental_and_molecular_modelling_data_from_the_stud... |
| Title | HECBioSim UK HPC Performance Benchmark Database |
| Description | This database contains a large number of performance benchmarks taken across the UK Tier1 and Tier2 HPC facilities with AMBER, GROMACS, LAMMPS and NAMD. These benchmarks are able to run across the wide variety of architectures available across the UK and report typical performance figures for a number of commonly used simulation protocols. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | This dataset assists PIs with applications for time across the many HPC facilities across the UK and gives the computing centers and the HECBioSim RAP a yard stick to measure requests for resource against the science case provided. These benchmarks have been used during the commissioning process of JADE2 to illustrate performance realised during the installation phase of the machine and were incorporated into the acceptance test schedule for Oxford University. |
| URL | http://www.hecbiosim.ac.uk |
| 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 collection of all membrane protein structures in their native lipid membranes. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2015 |
| Provided To Others? | Yes |
| Impact | Many fruitful collaborations with other scientists and workshops. Through further funding you have enabled us to keep this website live and fully functional. Sustainable research is essential! |
| URL | http://memprotmd.bioch.ox.ac.uk/ |
| 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 | Collaboration 2 with University of Virginia |
| Organisation | University of Virginia (UVa) |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Combination of Molecular simulations with Electron Paramagnetic Resonance studies to show the impact of binding of antibiotics to bacterial enzymes. |
| Collaborator Contribution | Electron Paramagnetic Resonance studies to show the impact of binding of antibiotics to bacterial enzymes. |
| Impact | Paper currently in preparation. Data presented at the Annual Biophysical Society Meeting in San Diego by our collaborator Prof Linda Columbus. |
| Start Year | 2019 |
| Description | Collaboration with Case Western |
| Organisation | Case Western Reserve University |
| Department | Department of Biochemistry |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Molecular simulations of the copper transporter CusA revealing how Copper stabilises the efflux state. We also show how the periplasmic domains change conformation from resting to extrusion state and also how protons may use a water wire across the membrane to power transport via the Proton Motive Force. |
| Collaborator Contribution | Ed Yu and his lab have provided novel structures of the CusA transporter in distinct states. |
| Impact | mBio publication now accepted. |
| Start Year | 2020 |
| 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 Pedro Carvalho |
| Organisation | University of Oxford |
| Department | Sir William Dunn School of Pathology |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Simulations of a key lipid-interacting protein. |
| Collaborator Contribution | Structures and Functional data. |
| Impact | Paper in progress. |
| Start Year | 2019 |
| 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. 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 Tanmay Bharat |
| Organisation | University of Oxford |
| Department | Sir William Dunn School of Pathology |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | My research team is simulating the biofilm matrix protein TasA from Bacillus subtilis based to evaluate protein-protein interactions that stabilise the higher order structures of the protein. |
| Collaborator Contribution | X-ray, electron cryomicroscopy and electron cryotomography data as of the wildtype protein as well as mutants based on our simulations |
| Impact | Manuscript has been submitted |
| Start Year | 2021 |
| Description | Collaboration with Tanmay Bharat |
| Organisation | University of Oxford |
| Department | Sir William Dunn School of Pathology |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Simulations of bacterial Surface Layer proteins. |
| Collaborator Contribution | Structures and functional data for SLPs |
| Impact | Structural basis of lipopolysaccharide mediated surface layer anchoring on Caulobacter crescentus cells Andriko von Kügelgen, Haiping Tang, Gail G. Hardy, Danguole Kureisaite-Ciziene, Yves V. Brun, Phillip J. Stansfeld, Carol V. Robinson, and Tanmay A.M. Bharat Cell pii: S0092-8674(19)31332-7. doi: 10.1016/j.cell.2019.12.006. A further publication is being finalised for submission. |
| Start Year | 2018 |
| Description | Collaboration with Trinity College Dublin |
| Organisation | Trinity College Dublin |
| Department | School of Biochemistry and Immunology |
| Country | Ireland |
| Sector | Academic/University |
| PI Contribution | Collaboration to study lipoprotein maturation and transport. We provide the molecular simulation and computational data to add value to our collaborators' structures. |
| Collaborator Contribution | Our collaborators provide the molecular structures and experimental data. |
| Impact | Publications, seminars and contribution to an international website resource. |
| Start Year | 2013 |
| 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 | Collaboration with University of Columbia |
| Organisation | Columbia University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Computational simulations and modelling to understand key biosynthetic pathways within the bacterial cell envelope. |
| Collaborator Contribution | Molecular structures of key biosynthetic enzymes. |
| Impact | Papers in progress. 1 paper ready for submission in Mar 2021. |
| Start Year | 2020 |
| 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 | ERNEST - European Research Network on Signal Transduction (CA18133) / Member of ERNEST Management Committee and the organizer of the first ERNEST Conference |
| Organisation | European Cooperation in Science and Technology (COST) |
| Department | COST Action |
| Country | Belgium |
| Sector | Public |
| PI Contribution | We were honoured to host the inaugural meeting of the European Research Network on Signal Transduction (ERNEST) funded by COST (Cooperation in Science and Technology) Action at Queen's University Belfast on October 28-30, 2019. PI was a main organizer of the GPCR meeting in Belfast. 150 delegates from 31 countries have attended the meeting, which made our conference a truly international event. This meeting was entitled "GPCR Pharmacology: Activation, Signalling and Drug Design" and focused on recent advances in knowledge and technology in the field. PI has designed the scientific program of the conference and has taken care of sponsor and venue arrangements. PDRA has gave a oral presentation on this BBSRC research project. |
| Collaborator Contribution | ERNEST COST Network has provided funding to organize the event. |
| Impact | Scientific outcomes of the meeting included recent advancements in cryo-electron microscopy, which is currently revolutionizing the field; how artificial intelligence and big data could drive pharmacology; the development of a multi-dimensional map of GPCR signal transduction and an overview of the IUPHAR / BPS Guide to PHARMACOLOGY database. The meeting had great networking opportunities and cultural experiences. On the first evening, a Welcome Reception with Deputy Lord Mayor Councillor Peter McReynolds, took place at the Belfast City Hall. The welcoming lectures were given by Michael Livingstone, a local historian, and Dr Aidan Seeley from the British Pharmacological Society. On the second evening, the Conference Dinner with traditional Irish dancing and music took place at the Great Hall. The conference has got additional sponsors: Belfast City Hall, Visit Belfast, British Pharmacological Society, ACS Pharmacology and Translational Science, Boehringer Ingelheim, Sosei Heptares, Nanotemper Technologies and Crelux, WuXi AppTec Company. As a result of this meeting, PI is a contributor to the ERNEST signalling map group. |
| Start Year | 2019 |
| Description | UCB Pharmaceuticals |
| Organisation | UCB Pharma |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Provision of molecular structures. |
| Collaborator Contribution | Assessment of the structures. |
| Impact | Continued direct impact between academia and pharmaceuticals. |
| Start Year | 2017 |
| Description | University of Virginia |
| Organisation | University of Virginia (UVa) |
| Department | School of Medicine |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Molecular simulations of molecular structures solved by the Zimmer research group. |
| Collaborator Contribution | Provision of novel molecular protein structures. |
| Impact | Understanding of the mechanisms of polysaccharide transport. |
| Start Year | 2018 |
| Description | collaboration with Dr.Chantal Valeriani |
| Organisation | Complutense University of Madrid |
| Country | Spain |
| Sector | Academic/University |
| PI Contribution | We have collaborated with Dr Valeriani and her team on the behaviour of different water models in simulations of aquaporins. We contributed expertise in water models and simulations of nanopores. This has resulted in a joint publication in J Chem Phys. |
| Collaborator Contribution | Dr. Valeriani's post doc Dr Miguel Angel Gonzalez visited Oxford for a few weeks and worked alongside Dr Lynch (the EPSRC postdoc on this project). We have continued the collaboration online and a paper has been published in J Chem Phys. |
| Impact | This has resulted in a joint publication in J Chem Phys. |
| Start Year | 2018 |
| Title | CG2AT2 |
| Description | An enhance version of our method to convert a coarse-grained system to atomic detail. https://github.com/pstansfeld/cg2at |
| Type Of Technology | Software |
| Year Produced | 2021 |
| Open Source License? | Yes |
| Impact | Becoming widely used within our research group and those that that are linked to our work. Aims to publish in the near future and induce world-wide usage. |
| Title | Computational tool to predict allosteric sites in membrane proteins |
| Description | The jupyter notebook scripts to set up the mapping of allosteric sites in GPCRs used in the paper: Probe Confined Dynamic Mapping for GPCR Allosteric Site Prediction Ciancetta A., Gill A.K., Ding T., Karlov D.S., Chalhoub G., McCormick P.J. and Tikhonova I.G. ACS Central Science, 2021 in press https://doi.org/10.1021/acscentsci.1c00802 The automatic procedure of probe confined dynamic mapping is provided as jupyter notebooks (MIDAS_EC.ipynb, MIDAS_IC.ipynb, and MIDAS_LI.ipynb) available. The required input files are (i) pdb of a receptor (preoriented with OPM), membrane, and one copy of cosolvent/fragment structures and (ii) an input file containing the following information: a receptor, an orthosteric ligand (if applicable), cosolvent and membrane file names (1); an orthosteric ligand (if applicable), cosolvent, and lipid residue names (2); cosolvent/fragment molecular weight and desired water/probe m/m % (in the closed box) (3); and height of the water buffer region between the protein and the water/probe mixture box (4). |
| Type Of Technology | New/Improved Technique/Technology |
| Year Produced | 2021 |
| Open Source License? | Yes |
| Impact | The product has received press coverage and new research collaborations. https://www.qub.ac.uk/News/Allnews/Newcomputermodellingcouldboostdrugdiscovery.html |
| URL | https://github.com/irinat12/Probe-Confined-Dynamic-Mapping-Protocols-GPCRs_membrane_proteins |
| 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 | Free Energy calculation methods for Lipid-Protein Interactions |
| Description | We have developed new tools for studying lipid-protein interactions. https://github.com/owenvickery/metadynamics_analysis https://github.com/owenvickery/umbrella_sampling |
| Type Of Technology | New/Improved Technique/Technology |
| Year Produced | 2019 |
| Impact | For further details see: Insights into Membrane Protein-Lipid Interactions from Free Energy Calculations. Corey RA, Vickery ON, Sansom MSP, Stansfeld PJ. J Chem Theory Comput. 2019 Oct 8;15(10):5727-5736. doi: 10.1021/acs.jctc.9b00548. |
| URL | https://github.com/owenvickery/metadynamics_analysis |
| Title | HECBioSim Automated Benchmarking Suite |
| Description | The automated benchmarking suite is a set of performance benchmarks and a set of Python utilities that integrate with our Longbow tool to provide an automated benchmarking tool. The benchmarks in this suite have been updated and tested to work with the latest software versions of AMBER, Gromacs, LAMMPS and NAMD. The utilities are both CPU and GPU aware and can profile the architectures using different regimes. This allows us to rapidly profile new and existing equipment for performance and can be used to monitor performance of software over time. |
| Type Of Technology | Software |
| Year Produced | 2021 |
| Open Source License? | Yes |
| Impact | This tool has been used in profiling the ARCHER2 4 cabinet system and has been used to profile the UK Tier2 machines JADE, JADE2, Bede, ISAMBARD, THOMAS and DIRAC to collect performance information. This performance information has been used during the commissioning phase of JADE2 and Bede and is also used to inform the HECBioSim resource allocation panels. |
| URL | http://www.hecbiosim.ac.uk |
| Title | HECBioSim Web Portal Upgrade |
| Description | The HECBioSim web portal provides a clean and simple way for us to interact with our community. It serves as a single place in which members of the bio-simulation community can get access to all of the things we offer; whether this be finding out about/applying for time on ARCHER, downloading our software tools, getting support with using HPC or our software, this web portal provides users with a single and consistent point of entry to what we have to offer. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2021 |
| Impact | The infrastructure that the HECBioSim portal was based was getting old and becoming a security risk, and was becoming unreliable and resulting in down-time. The Hardware had degraded to a point that the underlying operating system could no longer be updated and this brought with it challenges in maintaining a web facing resource. This refresh brought the web portal up to modern microservices style approach that is consistent with hosting in a cloud environment, thus allowing more flexibility going forward, this eliminates being tied to a particular generation of hardware and software and will allow us to deliver better more scalable and sustainable services going forward. |
| URL | http://www.hecbiosim.ac.uk |
| Title | HECBioSim Web Portal refresh |
| Description | The HECBioSim web portal provides a clean and simple way for us to interact with our community. It serves as a single place in which members of the bio-simulation community can get access to all of the things we offer; whether this be finding out about/applying for time on ARCHER, downloading our software tools, getting support with using HPC or our software, this web portal provides users with a single and consistent point of entry to what we have to offer. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2020 |
| Impact | The website was given a new look and feel as part of the new grant and also as part of a drive to modernise the way it behaves on recent browsers. Old features were retired and removed and new content added to reflect the new HPC resources that the HECBioSim got access to. More information was added to assist PIs in applying for resources through the HEC and information was added to support users of the Tier2 facility JADE in how to run their simulations. |
| URL | http://www.hecbiosim.ac.uk |
| Title | Lipoprotein Modification Tool |
| Description | We have developed a method to automatically modify lipoprotein cysteine residues. |
| Type Of Technology | Software |
| Year Produced | 2020 |
| Impact | This forms part of this paper: Characterising Membrane Association and Periplasmic Transfer of Bacterial Lipoproteins through Molecular Dynamics Simulations Shanlin Rao, George Bates, Callum Matthews, Owen Vickery, Phillip J. Stansfeld Structure The tool is here: https://github.com/owenvickery/add_acyl_tails_martini_2.2 |
| URL | https://www.sciencedirect.com/science/article/pii/S0969212620300125 |
| Title | Longbow v1.5.0 |
| Description | Longbow is an automated simulation submission and monitoring tool. Longbow is designed to reproduce the look and feel of using software on the users local computer with the difference that the heavy lifting is done by a supercomputer. Longbow will automatically generate the necessary submit files and handle all initial file transfer, monitor jobs, transfer files at configurable intervals and perform final file transfer and cleanup. Longbow can be used to launch one-off jobs, generate ensembles of similar jobs or even run many different jobs over many different supercomputers. Out of the box, Longbow is currently supporting the PBS/Torque, LSF, SGE, Slurm, SoGE schedulers and ships with application plugins for commonly used bio-molecular simulation softwares AMBER, CHARMM, GROMACS, LAMMPS, NAMD. Longbow is however highly configurable and will function normally with generic software without plugins, however plugins can easily be made to extend Longbow to fully support applications and schedulers that do not ship out of the box. Longbow is also available to developers of applications which require support for automating job submission. Longbow is available as a convenient and light-weight python API that can be integrated in a number of different way. |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | Longbow has been downloaded by 6,211 times world wide by researchers doing biomolecular simulation. Longbow simplifies the transfer, preparation and submission of simulations across a wide range of HPC architectures. Users at the beginner end of the spectrum can quickly be up and running on any HPC resource within minutes without having to learn much about the process of doing it. Power users can leverage the power of Longbow in generating huge arrays of simulations and have it fire and bring back results across multiple machines that they have access to. It is a tool mainly aimed at taking the pain out of HPC by automating the time consuming tedious tasks associated with doing it at scale. |
| URL | http://www.hecbiosim.ac.uk/longbow |
| Title | Longbow v1.5.1 |
| Description | Longbow is an automated simulation submission and monitoring tool. Longbow is designed to reproduce the look and feel of using software on the users local computer with the difference that the heavy lifting is done by a supercomputer. Longbow will automatically generate the necessary submit files and handle all initial file transfer, monitor jobs, transfer files at configurable intervals and perform final file transfer and cleanup. Longbow can be used to launch one-off jobs, generate ensembles of similar jobs or even run many different jobs over many different supercomputers. Out of the box, Longbow is currently supporting the PBS/Torque, LSF, SGE, Slurm, SoGE schedulers and ships with application plugins for commonly used bio-molecular simulation softwares AMBER, CHARMM, GROMACS, LAMMPS, NAMD. Longbow is however highly configurable and will function normally with generic software without plugins, however plugins can easily be made to extend Longbow to fully support applications and schedulers that do not ship out of the box. Longbow is also available to developers of applications which require support for automating job submission. Longbow is available as a convenient and light-weight python API that can be integrated in a number of different way. |
| Type Of Technology | Software |
| Year Produced | 2019 |
| Open Source License? | Yes |
| Impact | Longbow has been downloaded by 7,542 times world wide by researchers doing biomolecular simulation. Longbow simplifies the transfer, preparation and submission of simulations across a wide range of HPC architectures. Users at the beginner end of the spectrum can quickly be up and running on any HPC resource within minutes without having to learn much about the process of doing it. Power users can leverage the power of Longbow in generating huge arrays of simulations and have it fire and bring back results across multiple machines that they have access to. It is a tool mainly aimed at taking the pain out of HPC by automating the time consuming tedious tasks associated with doing it at scale. |
| URL | http://www.hecbiosim.ac.uk/longbow |
| Title | Longbow v1.5.2 |
| Description | Longbow is an automated simulation submission and monitoring tool. Longbow is designed to reproduce the look and feel of using software on the users local computer with the difference that the heavy lifting is done by a supercomputer. Longbow will automatically generate the necessary submit files and handle all initial file transfer, monitor jobs, transfer files at configurable intervals and perform final file transfer and cleanup. Longbow can be used to launch one-off jobs, generate ensembles of similar jobs or even run many different jobs over many different supercomputers. Out of the box, Longbow is currently supporting the PBS/Torque, LSF, SGE, Slurm, SoGE schedulers and ships with application plugins for commonly used bio-molecular simulation softwares AMBER, CHARMM, GROMACS, LAMMPS, NAMD. Longbow is however highly configurable and will function normally with generic software without plugins, however plugins can easily be made to extend Longbow to fully support applications and schedulers that do not ship out of the box. Longbow is also available to developers of applications which require support for automating job submission. Longbow is available as a convenient and light-weight python API that can be integrated in a number of different way. |
| Type Of Technology | Software |
| Year Produced | 2019 |
| Open Source License? | Yes |
| Impact | Longbow has been downloaded by 8,695 times world wide by researchers doing biomolecular simulation. Longbow simplifies the transfer, preparation and submission of simulations across a wide range of HPC architectures. Users at the beginner end of the spectrum can quickly be up and running on any HPC resource within minutes without having to learn much about the process of doing it. Power users can leverage the power of Longbow in generating huge arrays of simulations and have it fire and bring back results across multiple machines that they have access to. It is a tool mainly aimed at taking the pain out of HPC by automating the time consuming tedious tasks associated with doing it at scale. |
| URL | https://www.hecbiosim.ac.uk/downloads |
| Title | MemProtMD methods for membrane self-assembly and insertion |
| Description | A methodology for inserting a membrane protein into a lipid bilayer using Google Colab Notebooks. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2022 |
| Open Source License? | Yes |
| Impact | Regular usage within the research group and university teaching. |
| Title | OpenMMSLICER |
| Description | scientific software for sequential monte carlo simulations in openmm |
| Type Of Technology | Software |
| Year Produced | 2022 |
| Impact | This software has been further developed for simulated tempering and is being used for new research projects |
| URL | https://github.com/openmmslicer/openmmslicer |
| 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 | 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 |
| 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 | An introduction to Longbow |
| 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 | The HECBioSim CoSeC developer James Gebbie-Rayet gave a workshop on how to use Longbow with ARCHER as part of the CCPBioSim training week. The workshop was attended by 22 people and they learnt the basics of submitting simulations to ARCHER using our simulation automation tool. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.ccpbiosim.ac.uk/events/workshop-course-material/eventdetail/120/-/ccpbiosim-training-wee... |
| 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 | CCPBioSim Training Week - An introduction to software and hardware for biomolecular simulation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | This activity was a talk on the basics of biomolecular simulation software and the hardware landscape available to scientists. It was attended by around 200 delegates and was pitched at postgraduate researchers within the first 6 months of their studies. It discussed the basic hardware differences and the considerations for running software in various ways on these hardware types. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.ccpbiosim.ac.uk/events/workshop-course-material/eventdetail/127/-/training-week-2020 |
| Description | CCPBioSim Training Week - An introduction to software and hardware for biomolecular simulation |
| 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 | This was a hands-on workshop in which around 200 delegates attended virtually from around the world. The workshop was a basic introduction into setting up their own workstation for biomolecular simulation. This was a look at virtual machines and the installation of the most common tools and utilities used for the setup, running and analysis of biomolecular simulation. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.ccpbiosim.ac.uk/events/workshop-course-material/eventdetail/127/-/training-week-2020 |
| Description | Cardiff Scientific Society Lecture - public lecture online |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | 9 February 2022 Cardiff Scientific Society Lecture - public lecture online Title: Folding a Protein: Nature's Origami |
| Year(s) Of Engagement Activity | 2022 |
| 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 | GPUs for biomolecular researchers: an overview of accelerated computing, plus a deep dive into GROMACS on GPU |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | This event was an industrial talk from NVidia on getting the best out of running biomolecular simulations on the GPU and a general talk about GPUs and how they are different from other architectures. HECBioSim members also sat on a discussion panel where information was discussed about what machines are available around the UK and how to get access to them. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.hecbiosim.ac.uk/events/training-talks |
| Description | Hamied Foundation UK-India Antimicrobial Resistance Meeting 2019 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I was part of an expert panel of scientists and medics from the UK and India assembled to discuss how we can (a) combat existing antimicrobial resistance and (b) prevent or slow down the development of resistance in future. The chief medical officer of the UK was also in attendance and a gave talk. Collaborations between scientists from both countries were established and existing ones were strengthened. An emerging theme was that all levels must be addressed, from atoms and molecules through to patients, communities and the environment. I helped establish this theme. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://acmedsci.ac.uk/more/events/hamied-foundation-uk-india-antimicrobial-resistance-meeting-2019 |
| Description | Hands on demonstrations of Longbow at CCPBioSim 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 | At the CCPBioSim annual conference we had a stand at the poster sessions and throughout the programme where we show cased Longbow and offered advice to PIs about how to apply for simulation time and to users of HPC advice on performance. This proved quite popular with lots of requests for more of this kind of participation in the future. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.ccpbiosim.ac.uk/events/past-conferences/eventdetail/119/-/7th-annual-ccpbiosim-conferenc... |
| 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 | Linacre Lecture, University of Cambridge, in person. Title: Folding a Protein: Nature's Origami, 15 February 2022 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Linacre Lecture, Cambridge, for undergraduates, postgraduates, postdocs, PIs and for outreach and general interest |
| Year(s) Of Engagement Activity | 2022 |
| 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 | 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 | Queen's Computational Biology Club Symposium. Almudena Pino-Angeles |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Poster: Tracing the allosteric binding pathways to the cell membrane-GPCR interface. Discussions with bioinformaticians and appreciation of the application of AI in GPCR research. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Seeing is Believing: Build a DIY microscope!, Discovery Zone at York Festival of Ideas, UK |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Family friendly stand at the Science Fair 'Discovery Zone' at York Festival of Ideas, UK |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://yorkfestivalofideas.com/2023/calendar/discovery-zone/ |
| 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 | Training workshop |
| 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 | 12 early career researchers (mainly a mixture of PhD students and PDRAs) attended a 1-day workshop in Leeds organised by CCPBioSim/HECBioSim to learn how to use the computational workflows package "Crossflow" that was developed during this grant. The objective was to raise awareness of the software and promote its usage on the national supercomputing service ARCHER2. |
| Year(s) Of Engagement Activity | 2023 |