SI2-CHE: CCP-SAS - Collaborative Computational Project for advanced analyses of structural data in chemical biology and soft condensed matter

Lead Research Organisation: University College London
Department Name: Structural Molecular Biology

Abstract

The major infrastructural investment by the US and UK in high brilliance multiuser X-ray synchrotrons and neutron sources during the last two decades has been immensely successful in allowing external (university and commercial) users to exploit these facilities for data collection on ever more challenging and important systems. Of particular significance is the field of macromolecular crystallography (MX) where the hardware investment (eg: the UK Diamond Light Source alone has six MX stations) has also benefitted from large-scale, integrated, software development, maintenance and distribution largely through the CCP4 initiative. The result has been an explosion of new crystal structure data. The equivalent revolution is now needed to advance chemical biology and soft condensed matter research because the world around us is not one of static structures. To realize the full benefit of the instrumental investment for novel engineering and material science applications requires integrating the plethora of X-ray and neutron data with user-friendly, high-throughput, molecular modelling of the data, in order to reveal how structure in these systems changes in time and space with varying experimental conditions. This is the issue that defines the Grand Challenge to be tackled through this proposal.

The collaboration is motivated by the recognized importance of structural modelling at the large multiuser synchrotron and neutron facilities in both the US and the UK. Outside of biological macromolecules, soft condensed matter science has traditionally worked with relatively simple model systems. However, in recent years there has been a rapid increase in the complexity of colloid and polymer science as researchers strive to produce marketable materials, triggering a critical need for new integrated molecular modelling procedures to explain experimental data sets. Because these computational analyses are typically performed by individuals at their external institutions, progress in interpretation has, unsurprisingly, been much slower than witnessed in macromolecular crystallography. Here, by linking computational expertise at the multiuser facilities with experienced external laboratories that need to model diverse data sets, we are ideally positioned to develop the necessary procedures and infrastructure.

The intellectual merit of this proposal lies in the development of both new algorithms for more accurately and rapidly analysing structural data and the software infrastructure that will enable rapid and encompassing modelling of data obtained from complementary disciplines such as small angle X-ray and neutron scattering (SAXS and SANS), wide angle scattering, analytical ultracentrifugation (AUC) and NMR spectroscopy. Indeed the combination of different experimental methods provides new insights not available from one method alone. The significant advances in high end computational molecular modelling and simulation provide an exciting opportunity to create a software infrastructure for modelling which can make accessible the daunting information content from the combination of different techniques. The US and UK teams bring together colloid scientists, bioengineers and computational chemists, with experts in SAXS, SANS, AUC, NMR, and high performance computing (HPC) and its computing infrastructure for this challenge in macromolecular and supramolecular chemistry.

The broader impact of our multifaceted approach will result from the application of high-end molecular modelling using the data from the various in-situ structural probes as constraints. The goal will be to provide the software environment to enable multidisciplinary experimental teams to gain a detailed understanding of complex chemical interactions and how they shape structural organization. This has the potential, if successful, to transform the way soft matter science is done, and to dramatically accelerate the discovery process in these important fields.

Planned Impact

WHO WILL BENEFIT? The modelling software will be harnessed to present a diverse range of molecular models important for applications in industry. The time scale for these developments will be short, medium and long term. Companies working with bioengineering of antibodies - UCB and Lonza in Slough - UK; Genentech - USA) will benefit by being enabled to create molecular models of their macromolecules in diverse bioprocessing conditions. Unilever/Proctor& Gamble and other companies making personal care products stabilized by polymers/surfactants/lipids and containing complex mixtures of particles, emulsions & soluble species will benefit. They particularly rely on the powers of using multiple neutron contrasts to highlight/conceal various parts of complex structures. This is particularly true in the case of bio-derived surfactants which include protein/lipid components (eg: hydrophobins, surfactins etc). Companies involved in the design of novel bio-materials (tissue engineering; medical implants) may include GSK, Astrazeneca and Pfizer, and medical device manufacturers like Europlaz Technologies and Osteotec. Benefits to the NHS relate to the possibility of improving the bioengineering of therapeutic antibodies by reducing their production costs; the availability of more effective medication will be vital in terms of stretched NHS budgets. The improved understanding of micelle/polymer gel-based cleaning materials used on artworks/historical artefacts for preservation will benefit (eg: the polymer infiltration of wood a la Mary Rose). If the molecular structures of natural materials become accessible to SAXS/SANS, their modelling may offer insights into preservation processes and their optimisation.

HOW WILL THEY BENEFIT? The research will fundamentally alter the way in which reduced SAXS and SANS data are processed. By providing SAXS and SANS users with an easy-to-use tool to create molecular models from their data, the outcome will reveal clearer pictures of the entities they are working with. This will significantly facilitate an understanding of the chemical entity under study. This understanding will continue to improve as academic beneficiaries in the UK refine their predictive models of the SAXS-SANS data. Applications of the resulting molecular structural models are broad ranging. The development of new soluble polymers will benefit industries interested in rheology control (personal care, paints, drilling fluids, cleaning products, foods), triggered and controlled delivery for therapeutics, foods, flavours, perfumes, pesticides (nanostructured particles, self-assembling multicomponent vesicles), composite formation (polymer adsorption to particles for compatibilising particles into blends, solutions, gels etc, and applications ranging from aerospace lightweight composite materials to stronger carbon nanotube reinforced sporting gear).

The UK economy will benefit because this academic research will complement the UK's strengths in soft condensed matter research. Collaboration between chemists, physicists and computational modellers on soft condensed matter systems will ensure effective knowledge and skills transfer between physical chemistry and UK industry. This will expand its position in the global healthcare market and attract further R&D investment from global business which recognises the UK as a good place to conduct these activities. Such retention of expertise, know-how and intellectual property will aid the UK's capacity to remain internationally competitive.

BENEFITS FROM SKILLS TRAINING: The postdoctoral researcher (PDRA) will gain experience at the interface between protein or lipids interactions, physics, crystallography, molecular graphics modelling and industrial applications of this work. This will provide a sound basis for an academic or industrial career in soft condensed matter.

Publications

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Arunmanee W (2016) Gram-negative trimeric porins have specific LPS binding sites that are essential for porin biogenesis. in Proceedings of the National Academy of Sciences of the United States of America

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Bowerman S (2019) BEES: Bayesian Ensemble Estimation from SAS. in Biophysical journal

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Brookes E (2016) GSoC 2015 student contributions to GenApp and Airavata GSoC 2015 Student Contributions to GenApp and Airavata in Concurrency and Computation: Practice and Experience

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Castañeda CA (2016) Linkage via K27 Bestows Ubiquitin Chains with Unique Properties among Polyubiquitins. in Structure (London, England : 1993)

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Castañeda CA (2016) Linkage-specific conformational ensembles of non-canonical polyubiquitin chains. in Physical chemistry chemical physics : PCCP

 
Description Key Findings:
Discoveries: The successful delivery of a new and extensible analysis toolbox for the atomistic modelling of X-ray and neutron solution scattering data from biological and soft matter systems. Features a user-friendly web portal, HPC-/Cloud-ready computational backend, and modular architecture to facilitate community development. A review that summarises this toolbox was published by Perkins et al. [14 co-authors] (2016) in J Appl. Cryst.
Exploitation Route Taken Forward: The routine ability to develop atomistic structural models that describe X-ray and neutron small-angle solution scattering data will be a game changer for data analyses. The completion of this work paves the way for an expansion of CCP-SAS to address problems in biology and soft matter research that current methods of analysis find challenging. Companies involved in the EPSRC/BBSRC BioProNet and TSB/InnovateUK CAF networks have already expressed an interest in this software. However, further funding will be required to realise the full potential of CCP-SAS.
Sectors Aerospace, Defence and Marine,Agriculture, Food and Drink,Chemicals,Environment,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

URL http://www.ccpsas.org/
 
Description Findings: We have delivered a new, extensible, web-based software toolkit (CCP-SAS) for the computation of ensembles of atomistic structural models to describe X-ray and neutron solution scattering data acquired on biological and soft matter systems. Details are maintained on our website: www.ccpsas.org. As of March 2019 the project has generated 56 journal publications (30 in structural biology, 12 on the software development, 7 in biophysics, 5 on the underlying techniques, and 2 in polymer physics) and 67 oral presentations at scientific conferences and workshops in just over 5 years. We have also run 4 joint UK-USA user-community workshops and an interim strategy meeting (2 in the US, 2 in the UK, and the interim in Germany), and delivered 22 training sessions (9 in the UK, 6 in the US, 2 in India, 1 each in Pakistan, France and Australia, and 2 via videoconference). The toolkit has already been used to characterize commercially-produced monoclonal antibody fragments. The GenApp framework underlying CCP-SAS attracted resource from the Google Summer of Code programme, and an invitation to integrate with the Apache Software Foundations Airavata project.
First Year Of Impact 2013
Sector Agriculture, Food and Drink,Chemicals,Energy,Environment,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology
Impact Types Economic

 
Description BBSRC LIDO PhD CASE Research PhD Studentship
Amount £100,000 (GBP)
Funding ID BB/M009513/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2017 
End 09/2021
 
Description BBSRC LIDO PhD Research Studentship
Amount £100,000 (GBP)
Funding ID BB/M009513/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 06/2016 
End 09/2019
 
Description Fight For Sight-University College London IMPACT PhD studentship award.
Amount £73,044 (GBP)
Organisation University College London 
Sector Academic/University
Country United Kingdom
Start 01/2015 
End 12/2019
 
Description Joint EPSRC CDT- ISIS-Diamond PhD studentship
Amount £89,877 (GBP)
Organisation University College London 
Department Biochemical Engineering
Sector Academic/University
Country United Kingdom
Start 10/2016 
End 09/2020
 
Description Mizutani Foundation for Glycoscience Project Grant
Amount $40,000 (USD)
Funding ID 180218 
Organisation Mizutani Foundation for Glycoscience 
Start 04/2018 
End 03/2019
 
Description PhD studentship award
Amount £127,660 (GBP)
Organisation Government of Punjab 
Sector Public
Country India
Start 11/2016 
End 10/2019
 
Description UCL Capital Equipment Fund Call 2
Amount £279,038 (GBP)
Organisation University College London 
Sector Academic/University
Country United Kingdom
Start 12/2018 
End 12/2018
 
Description University College London
Amount £29,905 (GBP)
Funding ID Grant Reference EP/R511638/1. Project reference KEIF 2017-2020 
Organisation University College London 
Sector Academic/University
Country United Kingdom
Start 11/2018 
End 04/2019
 
Description A Joint EPSRC-NSF Software Infrastructure for Scientific Innovation Project 
Organisation National Science Foundation (NSF)
Country United States 
Sector Public 
PI Contribution The EPSRC and NSF have funded a joint proposal. This develops CCP-SAS software through a joint EPSRC (EP/K039121/1) and NSF (CHE-1265821) grant
Collaborator Contribution The UK and USA teams are developing new methods for the application of atomistic modelling for computing X-ray and neutron scattering curves
Impact 51 publications to date in which CCP-SAS contributed at least in part, and 58 oral presentations at scientific conferences and workshops to date (March 2018)
Start Year 2013
 
Title CCP-SAS - SASSIE 
Description Software for atomistic modelling of X-ray and neutron scattering curves 
Type Of Technology Software 
Year Produced 2014 
Open Source License? Yes  
Impact 51 publications to date 
URL http://www.ccpsas.org/index.html
 
Title CCP-SAS- SCT 
Description SCT calculates scattering curves for macromolecules starting from atomic coordinates 
Type Of Technology Software 
Year Produced 2014 
Open Source License? Yes  
Impact The community will be able to use this within SASSIE to compute scattering curves 
URL http://www.ccpsas.org/
 
Description 'Neutrons and Biology' School of the French Neutron Society, Carqueiranne (France) on September 16-19, 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact J S Bhatt (the postdoc on the EPSRC grant) gave a talk on. Molecular dynamics combined with SANS. 'Neutrons and Biology' School of the French Neutron Society, Carqueiranne (France) on September 16-19, 2018. Invited talk to the neutron society in France, explaining how molecular dynamics and Monte Carlo methods are applied to model scattering data.
Year(s) Of Engagement Activity 2018
 
Description 15th European Meeting on Complement in Human Disease in Uppsala, Sweden June 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact TALK. Ruodan Nan, Christopher M. Furze, David W. Wright, Jayesh Gor, Russell Wallis, and Stephen J. Perkins (2015) The flexible solution structures of mannose-binding lectin-associated serine proteases-1 and -2 provide novel insight on lectin pathway activation. 15th European Meeting on Complement in Human Disease in Uppsala, Sweden 27-30 June 2015.

POSTER. Ka Wai Fung, Ruodan Nan, Kashif Butt, Marcus J. Swann, and Stephen J. Perkins (2015) The bivalent and co-operative molecular mechanism of Factor H binding to a heparin-coated surface accounts for the onset of inflammatory diseases. 15th European Meeting on Complement in Human Disease in Uppsala, Sweden 27-30 June 2015. Awarded Best poster prize.
Year(s) Of Engagement Activity 2015
URL https://akkonferens.slu.se/emchd2015/
 
Description 3rd Annual Joint US-UK CCP-SAS Project Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This Workshop follows on from the previous two workshops at NIST in February 2014 and Diamond in October of 2014 and the interim closed project meeting held at SAS-2015 in Berlin in September 2015. The Workshop consisted of three parts. On Monday were the presentation sessions of broad interest to the scientific community. Attendees were encouraged to bring posters explaining their use of these kinds of modeling techniques or illustrating their need for such. Tuesday morning was devoted to a meeting between the CCP-SAS project and individuals or institutions with activities in related software development areas, interests in participating in the CCP-SAS current or projected activities and facilities with potential interest in deploying CCP-SAS products on their servers for use by their users and thus have a potential interest in helping with maintenance activities. Discussions focussed on current activities, directions and needs with a goal of elucidating adjustments to CCP-SAS activities in the remaining funding cycle, and, more importantly of developing collaborations with other projects and identifying areas for joint funding applications moving forward.

Talk - Gar Kay Hui and Stephen J Perkins. Comparison of SASSIE modelling outcomes for the human antibodies IgG1, IgG2 and IgG4
Year(s) Of Engagement Activity 2016
URL http://www.ccpsas.org/Meetings/Fourth/Program.html
 
Description 3rd Annual Joint US-UK CCP-SAS Project Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This Workshop follows on from the previous two workshops at NIST in February 2014 and Diamond in October of 2014 and the interim closed project meeting held at SAS-2015 in Berlin in September 2015. The Workshop will consist of three parts. On Monday will be the presentation sessions of broad interest to the scientific community. Attendees are encouraged to bring posters explaining their use of these kinds of modeling techniques or illustrating their need for such. Tuesday morning will be devoted to a meeting between the CCP-SAS project and individuals or institutions with activities in related software development areas, interests in participating in the CCP-SAS current or projected activities and facilities with potential interest in deploying CCP-SAS products on their servers for use by their users and thus have a potential interest in helping with maintenance activities. Discussions will focus on current activities, directions and needs with a goal of elucidating adjustments to CCP-SAS activities in the remaining funding cycle, and, more importantly of developing collaborations with other projects and identifying areas for joint funding applications moving forward.

Talk - Ka Wai Fung, David W. Wright, Marcus Swann and Stephen J. Perkins Complement C4b undergoes a conformational extension at its TED domain with increase in ionic strength at surfaces and in solution (now published in Biochemical Journal)
Year(s) Of Engagement Activity 2016
URL http://www.ccpsas.org/Meetings/Fourth/Program.html
 
Description A McClusky, B Morgan, S Parker & K J Edler. 2018/09/16 Introducing programming to undergraduate chemists: and the tools we've developed to help them, PYCON UK, Cardiff 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Undergraduate students
Results and Impact Teaching computing skills to students at Cardiff Univerity
Year(s) Of Engagement Activity 2018
 
Description A McClusky, S Parker & K Edler, Using high-performance computing and molecular dynamics to rationalise micelle structure from small-angle scattering, SAS2018 , Traverse City, Michigan 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This meeting is the main trienennial meeting for the international solution scattering community. Mr A McClusky was selected to give a talk about the application of SASSIE to model polymers thus promoting its greater uptake
Year(s) Of Engagement Activity 2018
URL https://sas2018.anl.gov/
 
Description A McClusky, S Parker & K J Edler, pylj: an open-source Python library for teaching the interaction between molecular simulation and scattering, SAS2018, Traverse City, Michigan  - IUCr Journals Prize for the Best Student Lecture, SAS2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This meeting is the main trienennial meeting for the international solution scattering community. Mr A McClusky was selected to give a talk about new computational methods for SASSIE in CCP-SAS to modelling polymer systems, thus promoting its greater uptake in the field. He was awarded the IUCr Journals Prize for the Best Student Lecture, SAS2018
Year(s) Of Engagement Activity 2018
URL https://sas2018.anl.gov
 
Description Annual CCP-BioSim Conference, Leeds, Jan 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact TALK. David W. Wright, Ruodan Nan, Gar-Kay Hui, Joseph Curtis, Emre Brookes and Stephen J. Perkins (2015) CCP-SAS - Novel Approaches for the Atomistic Modelling of Small Angle Scattering Data in Biology. 4th Annual CCP-BioSim Conference, Frontiers of Biomolecular Simulation, Leeds University, 7-9th January 2015
Year(s) Of Engagement Activity 2015
 
Description Biophysical Society Annual Meeting, Baltimore, Maryland, USA, February 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact TALK. David W. Wright, Ruodan Nan, Gar-Kay Hui, Joseph E. Curtis, Emre H. Brookes, Stephen J. Perkins (2015). CCP-SAS - NOVEL APPROACHES FOR THE ATOMISTIC MODELLING OF SMALL ANGLE SCATTERING DATA IN BIOLOGY. 59th Biophysical Society Annual Meeting, Baltimore, Maryland, USA, 7-11th February 2015
Year(s) Of Engagement Activity 2015
 
Description British Biophysical Society meeting, Warwick University, July 2014 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Ruodan Nan, Christopher M. Furze, David W. Wright, Russell Wallis, and Stephen J. Perkins (2014) The solution structures of MASP (mannose-binding lectin-associated serine protease) and MBL (mannose-binding lectin) provides insight on the activation of the lectin pathway of complement. British Biophysical Society 2014 Biennial Meeting, Warwick University, 9-11th July 2014.
Stephen J. Perkins, David W. Wright, Joseph E. Curtis and the CCP-SAS consortium (2014) CCP-SAS - a new community consortium for the atomistic modelling of SANS and SAXS data. British Biophysical Society 2014 Biennial Meeting, Warwick University, 9-11th July 2014.
Talk sparked questions and discussion afterwards

The talk on modelling of the complement MASP protein encouraged attendees to consider taking up CCP-SAS software
Year(s) Of Engagement Activity 2014
 
Description Faculty Lecture at Government College University, Lahore (24 Oct 2017) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact I gave a talk "Atomistic modelling of scattering data in CCP-SAS: new insights into antibody conformations" to PhD students and Faculty at Government College University Lahore, one of the 10 best-ranked universities in Pakistan (with two past Nobel Laureates). The talk generated much local interest and several PhD students came up afterwards to ask questions about CCP-SAS. Planning for possible grant applications were discussed to build CCP-SAS in Pakistan.
Year(s) Of Engagement Activity 2017
 
Description Faculty Lecture at Kinnaird College for Women University, Lahore, Pakistan (27 Oct 2017) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact I gave a talk "Atomistic modelling of scattering data in CCP-SAS: new insights into antibody conformations" to undergraduates, PhD students and Faculty at the Kinnaird College for Women University, a large university in Lahore founded by the British in 1913. The talk generated much local interest and several members of faculty came up afterwards to ask questions about CCP-SAS. I met the Vice-Chancellor.
Year(s) Of Engagement Activity 2017
 
Description Gar Kay Hui, ATOMISTIC X-RAY SOLUTION SCATTERING STRUCTURES OF HUMAN IGG1 AND IGG4 ANTIBODY-RECEPTOR COMPLEXES. XVII International Small Angle Scattering Conference - SAS2018. Grand Traverse Resort & Spa, Traverse City, Michigan, October 7-12, 2018. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This meeting is the main trienennial meeting for the international solution scattering community. Ms Hui was selected to give a talk about the application of SASSIE in CCP-SAS to modelling human antibody structures important in immunology and biotechnology, thus promoting its greater uptake.
Year(s) Of Engagement Activity 2018
URL https://sas2018.anl.gov/
 
Description International Conference on Molecular Recognition, Zaragoza, Spain, Feb 2016 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented talk entitled:CCP-SAS - a community consortium for the atomistic modelling of scattering data: example applications
Year(s) Of Engagement Activity 2016
URL http://bifi.es/events/bifi2016/?q=program
 
Description International Conference on Small-Angle Scattering, Berlin, Germany. September, 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact TALK. Joseph E. Curtis, Emre Brookes, David W. Wright, Hailiang Zhang, Jianhan Chen, Stephen M. King, Paul Butler, Stephen J. Perkins (2015) CCP-SAS - a community consortium for the atomistic modelling of scattering data. 16th International Conference on Small-Angle Scattering, 13-18 September, 2015, Berlin, Germany. Increased interest in CCP-SAS

TALK. David W. Wright, Gar Kay Hui. Owen L. Vennard, Lucy E. Rayner, Melissa Pang, See Cheng Yeo, Jayesh Gor, Karen Molyneux, Jonathan Barratt and Stephen J. Perkins (2015) The asymmetric solution structures of native and patient monomeric human IgA1 reveal new insights on IgA nephropathy. 16th International Conference on Small-Angle Scattering, 13-18 September, 2015, Berlin, Germany. Increased interest in CCP-SAS
Year(s) Of Engagement Activity 2015
URL https://www.helmholtz-berlin.de/events/sas/
 
Description Invited Keynote Lecture - 3rd International Conference on Biosciences (ICB-2018) from 9-11th May, 2018, GC University Lahore Pakistan 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact I gave an invited Keynote Lecture at a 3-day international conference at GC University Lahore Pakistan, sponsored by the Biological Society of Pakistan. The event attracted PhD students and PIs with a broad interest in biology, and enabled interactions between UK and Pakistan workers in this field. Planning for possible grant applications were discussed to build CCP-SAS in Pakistan
Year(s) Of Engagement Activity 2018
 
Description Invited talk at the Computation for Biomolecular Cryo-Electron Microscopy and Tomography Workshop, July 14, 2017, University of Leeds, UK 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact The Leeds meeting was organised by CCP-EM and CCP-Biosim. The CCP-SAS project was invited in order to give a short presentation of how we were making progress.
Year(s) Of Engagement Activity 2014,2017
 
Description Keynote lecture. International Conference on "Trends in Natural Science: from Basic to Applied". Lahore College for Women University, Oct 26, 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact I gave a Keynote Lecture "Atomistic modelling of scattering data in CCP-SAS: new insights into antibody conformations" at a 2-day international conference on "Trends in Natural Science: from Basic to Applied" scheduled from 25-27 October, 2017, organised by The society for promotion of Science and Technology in collaboration with the Higher Education Commission, Pakistan. The meeting was addressed by a Government Minister as well as the Vice-Chancellor. I was interviewed for the local radio station, and was photographed for the Lahore newspapers. The meeting was well attended by students from Pakistan and I had the opportunity to make links with academic colleagues there in several social events I attended.
Year(s) Of Engagement Activity 2017
 
Description Monte Carlo atomistic modelling of X-ray and neutron scattering data for human IgG1 and IgG4 antibodies reveals new insights on antibody solution structure and function, NIBGE, Faisalabad, Pakistan. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I gave an invited lecture to the prestigious National Institute for Biotechnology & Genetic Engineering, Faisalabad, Pakistan, attended by over 100 staff. Afterwards, I met group leaders and discussed how protein structure modelling could help with their projects. Planning for possible grant applications were discussed to build CCP-SAS in Pakistan
Year(s) Of Engagement Activity 2018
 
Description NOBUGS 2016 (Copenhagen) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The eleventh NOBUGS Conference was held at Thorvaldsensvej 40 in Copenhagen, Denmark on the 17th to 19th October 2016. The NOBUGS (New Opportunities for Better User Group Software) Conference Series has the aim to foster collaboration and exchange between scientists and IT professionals working on software for X-ray, neutron and muon sources around the world. NOBUGS 2016 was organised by the European Spallation Source, University of Copenhagen and MAX IV Laboratory.

We presented a poster: E Brookes, J Curtis, D Wright, H Zhang, P Butler, S Perkins, D Barlow, J Chen, K Edler, T Irving, S Kruer, D Scott, N Terrill and S. King. A New Paradigm for Data Analysis Workflows.
Year(s) Of Engagement Activity 2016
URL https://indico.esss.lu.se/event/357/
 
Description Neutron Characterisation in Fundamental and Applied Biotechnology - meeting in Abingdon Sept 2014 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact TALK. Stephen J. Perkins, Gar-Kay Hui and Lucy Rayner (2014) Atomistic modelling of SANS and SAXS data in applications to diverse antibody classes important in biotechnology and disease

Sparked discussion with industry
Year(s) Of Engagement Activity 2014
 
Description Neutron scattering group (Feb 18) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact This event was organised by the Neutron Scattering group of the IOP and RSC. "Neutrons and Global Challenges II: Health and Healthcare"
Held on 9th February 2018 at the Institute of Physics, 76 Portland Place, London W1B 1NT www.iop.org. The event attracted PhD students and PIs with an interest in neutron scattering, and enabled interactions between UK workers in this field. Two talks were given by David Scott and Stephen Perkins.
Year(s) Of Engagement Activity 2018
URL https://www.events.iop.org/e/neutrons-and-global-challenges-ii-health-and-healthcare-58c47b398f55462...
 
Description P. D. Butler, S. J. Perkins, D. W. Wright, H. Zhang, E. H. Brookes, J. Chen, T. C. Irving, S. Krueger, D. J. Barlow, K. J. Edler, D. J. Scott, N. J. Terrill, S. M. King, J. S. Bhatt, C. Jeong, and J. E. Curtis CCP-SAS - A COMMUNITY CONSORTIUM FOR THE ADVANCED MODELLING OF SCATTERING DATA XVII International Small Angle Scattering Conference - SAS2018. Grand Traverse Resort & Spa, Traverse City, Michigan, October 7-12, 2018. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Prof Butler presented a poster for the session which attracted much interest, in which the achievements of CCP-SAS were summarised.
Year(s) Of Engagement Activity 2018
URL https://sas2018.anl.gov
 
Description Pacifichem, 15 - 20th December 2015, Honolulu, Hawaii - Keynote lecture 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Title: Polymer stabilized phospholipid nanodiscs, in Symposium "Self-assembled Biofunctional Nanomaterials" (#433), Pacifichem, 15 - 20th December 2015, Honolulu, Hawaii (keynote lecture by Professor Karen Edler on CCP-SAS)
Year(s) Of Engagement Activity 2015
URL http://www.pacifichem.org/
 
Description Polymer Effects on Formation of Polymer-Stabilized Lipid Nanodiscs. Nanoparticle Technologies for Membrane Protein Research, Jun 27, 2017. Leeds, UK. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact CCP-SAS talk given by Prof K. Edler. Polymer Effects on Formation of Polymer-Stabilized Lipid Nanodiscs. Nanoparticle Technologies for Membrane Protein Research, Jun 27, 2017. Leeds, UK.
Year(s) Of Engagement Activity 2017
 
Description Recent Developments to the UltraScan SOlution MOdeler (US-SOMO) Software Suite. AUC 2017, Glasgow, Scotland, Jul 27, 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk given by E.H. Brookes, J. Pérez, P. Vachette, A. Savelyev, M. Rocco at the Glasgow AUC meeting in July 2017
Year(s) Of Engagement Activity 2017
 
Description S. J. Perkins, A. J. Osborne, R. Nan, A. Miller, J. S. Bhatt and J. Gor - DIFFERENT FOLDED-BACK MONOMERIC SOLUTION STRUCTURES FOR COMPLEMENT FACTOR H CLARIFY DISTINCT FUNCTIONS IN THE WILD-TYPE TYR402 AND DISEASE-RELATED HIS402 ALLOTYPES, XVII International Small Angle Scattering Conference - SAS2018. Grand Traverse Resort & Spa, Traverse City, Michigan, October 7-12, 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This meeting is the main trienennial meeting for the international solution scattering community. Prof Perkins was selected to give a talk about the application of SASSIE in CCP-SAS to modelling a major complement protein important in immunology and medicine, thus promoting its greater uptake
Year(s) Of Engagement Activity 2018
URL https://sas2018.anl.gov/
 
Description S.J.Perkins. Monte Carlo atomistic modelling of X-ray and neutron scattering data for the human complement proteins reveals new insights on structure and function in innate immunity. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact I gave an invited Keynote Lecture at a 3-day international conference at the LCWU. The event attracted PhD students and PIs with a broad interest in biology, and enabled interactions between UK and Pakistan workers in this field. Planning for possible grant applications were discussed to build CCP-SAS in Pakistan
Year(s) Of Engagement Activity 2018
 
Description SOCI, Swindon 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact his meeting focused on state-of-the-art applications of SANS across a range of Soft Matter systems, and the future scientific opportunities that will come from new facilities, new instruments, and technical advances. The meeting also celebrated the retirement of Dr Richard K Heenan, principal scientist in SANS at the ISIS Pulsed Neutron & Muon Source.

A poster was presented: Atomistic modelling of scattering curves in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS). Perkins et al.

The event took place at the STEAM - Museum of the Great Western Railway, Swindon and was attended by over 50 people. Conference papers are available on the web site.
Year(s) Of Engagement Activity 2016
URL http://www.soci.org/news/colloids/sans-past-papers-2016
 
Description Selected talk at the BioProNET 4th Annual Science Meeting, Oct 11, 2017 Warwick, UK. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The BioProNet meeting involves industry and academics across the UK, and the meeting included speakers from abroad (eg: Prof Chris Roberts, Delaware). We were selected to give a talk on CCP-SAS and its utility for industry. The talk went down well and we have been offered antibody samples for further study.
Year(s) Of Engagement Activity 2017
 
Description Talk given at the Practice and Experience in Advanced Research Computing Conference, Jul 9-13 2017. New Orleans, USA. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk given by E. Brookes & A. Savelyev, titled "GenApp Integrated with OpenStack Supports Elastic Computing on Jetstream".
Year(s) Of Engagement Activity 2017
 
Description Two talks, CCP-SAS meeting, Diamond, September 2014 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact TALKS. Stephen J Perkins Ruodan Nan. (2014) CCP-SAS Project Update. Update on MASP modelling. CCP-SAS 2nd Joint UK-USA Project Meeting, Diamond Synchrotron. 6-7 October 2014.

Presented our molecular modelling of MASP. Talk sparked questions and discussion afterwards

After the talk, it became possible to review how well our software worked in the modelling of the complement MASP protein.
Year(s) Of Engagement Activity 2014
 
Description XXVIth International Complement Workshop - CFHR5 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The 26th International Complement Workshop (XXVI ICW) held in the city of Kanazawa, Japan in September 2016 is the largest biannual complement meeting and attracts a broad range of attendees from basic immunochemistry to hospital clinicians.

We presented a poster - Nilufar Kadkhodayi-Kholghi, Jayesh Gor, Anna Ferlin, Lindsay C. McDermott, Daniel P. Gale, Stephen J. Perkins The solution structure of the human complement regulator CFHR5 reveals a compact dimeric structure by X-ray scattering and analytical ultracentrifugation
Year(s) Of Engagement Activity 2016
URL http://icwkanazawa2016.com/index.html
 
Description XXVth International Complement Workshop, Rio de Janeiro, Brazil Sept 2014 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact TALK. GIVEN BEST PRESENTATION AWARD. Elizabeth Rodriguez, Ruodan Nan, Keying Li, Jayesh Gor and Stephen J. Perkins (2014) A revised mechanism for the activation of complement C3 to C3b and a molecular explanation of the difference between their C3S and C3F polymorphic forms. XXVth International Complement Workshop, Rio de Janeiro, Brazil. 14-18th September 2014

Sparked questions and discussion afterwards.
Year(s) Of Engagement Activity 2014