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.
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.
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
Arturo EC
(2021)
Manipulation of a cation-p sandwich reveals conformational flexibility in phenylalanine hydroxylase.
in Biochimie
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
Barclay A
(2022)
Global fitting of multiple data frames from SEC-SAXS to investigate the structure of next-generation nanodiscs.
in Acta crystallographica. Section D, Structural biology
Bhojane PP
(2017)
Small Angle Neutron Scattering Studies of R67 Dihydrofolate Reductase, a Tetrameric Protein with Intrinsically Disordered N-Termini.
in Biochemistry
Boughton AJ
(2020)
Branching via K11 and K48 Bestows Ubiquitin Chains with a Unique Interdomain Interface and Enhanced Affinity for Proteasomal Subunit Rpn1.
in Structure (London, England : 1993)
Bowerman S
(2019)
BEES: Bayesian Ensemble Estimation from SAS.
in Biophysical journal
Brookes E
(2015)
The GenApp framework integrated with Airavata for managed compute resource submissions
in Concurrency and Computation: Practice and Experience
Brookes E
(2018)
Recent advances in the UltraScan SOlution MOdeller (US-SOMO) hydrodynamic and small-angle scattering data analysis and simulation suite.
in European biophysics journal : EBJ
Brookes E
(2013)
Fibrinogen species as resolved by HPLC-SAXS data processing within the UltraScan Solution Modeler (US-SOMO) enhanced SAS module.
in Journal of applied crystallography
Brookes E
(2023)
AlphaFold-predicted protein structures and small-angle X-ray scattering: insights from an extended examination of selected data in the Small-Angle Scattering Biological Data Bank.
in Journal of applied crystallography
Brookes E
(2019)
GenApp, Containers and Abaco
Brookes E
(2015)
GSoC 2015 student contributions to GenApp and Airavata
in Concurrency and Computation: Practice and Experience
Brookes E
(2016)
US-SOMO HPLC-SAXS module: dealing with capillary fouling and extraction of pure component patterns from poorly resolved SEC-SAXS data.
in Journal of applied crystallography
Brookes EH
(2023)
Beyond the US-SOMO-AF database: a new website for hydrodynamic, structural, and circular dichroism calculations on user-supplied structures.
in European biophysics journal : EBJ
Bush M
(2019)
An ensemble of flexible conformations underlies mechanotransduction by the cadherin-catenin adhesion complex.
in Proceedings of the National Academy of Sciences of the United States of America
Calyam P
(2020)
Measuring success for a future vision: Defining impact in science gateways/virtual research environments
in Concurrency and Computation: Practice and Experience
CastaƱeda C
(2016)
Linkage-specific conformational ensembles of non-canonical polyubiquitin chains
in Physical Chemistry Chemical Physics
CastaƱeda CA
(2016)
Linkage via K27 Bestows Ubiquitin Chains with Unique Properties among Polyubiquitins.
in Structure (London, England : 1993)
Castellanos MM
(2017)
Investigating Structure and Dynamics of Proteins in Amorphous Phases Using Neutron Scattering.
in Computational and structural biotechnology journal
Castellanos MM
(2018)
Characterization of the NISTmAb Reference Material using small-angle scattering and molecular simulation : Part I: Dilute protein solutions.
in Analytical and bioanalytical chemistry
Castellanos MM
(2017)
Characterization of Monoclonal Antibody-Protein Antigen Complexes Using Small-Angle Scattering and Molecular Modeling.
in Antibodies (Basel, Switzerland)
Castellanos MM
(2016)
Role of Molecular Flexibility and Colloidal Descriptions of Proteins in Crowded Environments from Small-Angle Scattering.
in The journal of physical chemistry. B
Castellanos MM
(2018)
Characterization of the NISTmAb Reference Material using small-angle scattering and molecular simulation : Part II: Concentrated protein solutions.
in Analytical and bioanalytical chemistry
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 2022 the project has generated 95 journal publications (61 in structural biology, 18 on the software development, 7 in biophysics, 6 on the underlying techniques, and 3 in polymer physics) and 77 oral presentations at scientific conferences and workshops in just over 7 years. We have also run 5 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 30 training sessions (13 in the UK, 10 in the US, 2 in France, India and Australia, 1 in Pakistan), and 3 more 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 | Ā£100,000 (GBP) |
Funding ID | BB/M009513/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 09/2017 |
End | 09/2021 |
Description | BBSRC LIDO PhD Research Studentship |
Amount | Ā£100,000 (GBP) |
Funding ID | BB/M009513/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 05/2016 |
End | 09/2019 |
Description | Fight For Sight-University College London IMPACT PhD studentship award. |
Amount | Ā£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 | Ā£89,877 (GBP) |
Organisation | University College London |
Department | Biochemical Engineering |
Sector | Academic/University |
Country | United Kingdom |
Start | 09/2016 |
End | 09/2020 |
Description | Mizutani Foundation for Glycoscience Project Grant |
Amount | $40,000 (USD) |
Funding ID | 180218 |
Organisation | Mizutani Foundation for Glycoscience |
Sector | Charity/Non Profit |
Country | Japan |
Start | 03/2018 |
End | 03/2019 |
Description | PhD studentship award |
Amount | Ā£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 | Ā£279,038 (GBP) |
Organisation | University College London |
Sector | Academic/University |
Country | United Kingdom |
Start | 12/2018 |
End | 12/2018 |
Description | University College London |
Amount | Ā£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 |
Title | SLDMOL: A tool for the structural characterization of thermally disordered membrane proteins |
Description | This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018) Abstract SLDMOL is a program for modeling the 1-D scattering length density (SLD) profile of proteins at the lipid membrane-solution interface or adsorbed to other surfaces. The program reads experimental SLD data from neutron or X -ray reflectivity measurements and compares the results to a trajectory of protein structures, finding the conformation and orientation that best fits the experimental data. SLDMOL is a freely distributed open source program written in python that can be run independently u... Title of program: SLDMOL Catalogue Id: AETX_v1_0 Nature of problem Reflectivity is a powerful technique to study the conformation of biological molecules at surface and interfaces. Open source software that facilitates computational modeling and interpretation of experimental results in terms of detailed molecular structure is currently lacking. Versions of this program held in the CPC repository in Mendeley Data AETX_v1_0; SLDMOL; 10.1016/j.cpc.2014.07.006 |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://data.mendeley.com/datasets/fdzgkn2kpk/1 |
Title | SLDMOL: A tool for the structural characterization of thermally disordered membrane proteins |
Description | This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018) Abstract SLDMOL is a program for modeling the 1-D scattering length density (SLD) profile of proteins at the lipid membrane-solution interface or adsorbed to other surfaces. The program reads experimental SLD data from neutron or X -ray reflectivity measurements and compares the results to a trajectory of protein structures, finding the conformation and orientation that best fits the experimental data. SLDMOL is a freely distributed open source program written in python that can be run independently u... Title of program: SLDMOL Catalogue Id: AETX_v1_0 Nature of problem Reflectivity is a powerful technique to study the conformation of biological molecules at surface and interfaces. Open source software that facilitates computational modeling and interpretation of experimental results in terms of detailed molecular structure is currently lacking. Versions of this program held in the CPC repository in Mendeley Data AETX_v1_0; SLDMOL; 10.1016/j.cpc.2014.07.006 |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://data.mendeley.com/datasets/fdzgkn2kpk |
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, MichiganĀ - 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 | SAS2018 International Conference, USA |
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 | Workshop and Talk - E. H. Brookes, J. Pérez, P. Vachette and M. Rocco, Advances to the Ultrascan Solution Modeler (US-SOMO) SAS and HPLC-SAXS modules. XVII International Small Angle Scattering Conference - SAS2018. Grand Traverse Resort & Spa, Traverse City, Michigan, October 7-12, 2018. |
Year(s) Of Engagement Activity | 2018 |
Description | SASSIE training course |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | We delivered a morning training session at the ISIS neutron facility on how to use molecular modelling (Monte Carlo; molecular dynamics) to fit scattering curves in terms of atomistic models |
Year(s) Of Engagement Activity | 2019 |
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 - Exploring the Relationship Between the Structure, Function, and Dynamics of Biomolecular Complexes |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Talk by Jeff Wereszczynski - Exploring the Relationship Between the Structure, Function, and Dynamics of Biomolecular Complexes - University of Delaware Department of Physics, February 2019 |
Year(s) Of Engagement Activity | 2019 |
Description | Talk - Exploring the Relationship Between the Structure, Function, and Dynamics of Biomolecular Complexes |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Talk - Jeff Wereszczynski - Exploring the Relationship Between the Structure, Function, and Dynamics of Biomolecular Complexes - West Virginia University Department of Chemistry, January 2019 |
Year(s) Of Engagement Activity | 2019 |
Description | Talk - Illinois |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Professional Practitioners |
Results and Impact | Talk - Jeff Wereszczynski - Exploring the Relationship Between the Structure, Function, and Dynamics of Biomolecular Complexes - Illinois Institute of Technology Department of Physics, September 2018 |
Year(s) Of Engagement Activity | 2018 |
Description | Talk - Temple University |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Professional Practitioners |
Results and Impact | Jeff Wereszczynski - Exploring the Relationship Between the Structure, Function, and Dynamics of Biomolecular Complexes - Temple University Department of Physics, April 2018 |
Year(s) Of Engagement Activity | 2018 |
Description | Talk at the CECAM meeting, ILL, France |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Talk - K. Edler - Micelles & Monolayers: Exploring use of models to understand scattering data. CECAM - Simulations of Small angle scattering for soft matter and life sciences. Institut-Laue-Langevin, Grenoble, France. 8-12 April 2019 |
Year(s) Of Engagement Activity | 2019 |
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 | US-SOMO and SASSIE2 workshops at the 24th International Analytical Ultracentrifugation Workshop and Symposium August 24-29, 2019 in Christchurch, NZ |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Brookes, Rocco and Perkins gave several training workshops at the 24th International Analytical Ultracentrifugation (AUC) Workshop in Christchurch, New Zealand. These covered the use of SOMO and SASSIE as research tools for the molecular modelling of AUC and scattering data sets |
Year(s) Of Engagement Activity | 2019 |
URL | https://auc2019.uleth.ca/ |
Description | Workshop and Talk on CCP-SAS |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | S. Perkins, J. Bhatt --- CCP-SAS - a community consortium for the advanced modelling of scattering data - applications and implementation. CECAM - Simulations of Small angle scattering for soft matter and life sciences. Institut-Laue-Langevin, Grenoble, France. 8-12 April 2019. Talk in main meeting. Workshop at the end of the meeting. |
Year(s) Of Engagement Activity | 2019 |
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 |