SI2-CHE: ExTASY: Extensible Tools for Advanced Sampling and analYsis
Lead Research Organisation:
University of Nottingham
Department Name: Sch of Pharmacy
Abstract
One of the biggest problems we face as we try to develop new materials and new medicines is the enormous gap between the size and complexity of the individual molecules that we understand and can manipulate through chemistry and physics, and the size and complexity of the materials we want to make or biological systems we wish to influence. Computer simulation methods are extremely useful for predicting the properties and behaviour of individual molecules - e.g. of a potential new polymer or a newly-discovered protein - but how will that behaviour relate to the real world situation when we have maybe 1,000,000,000,000,000,000,000 of them together? It is completely beyond the power of computers to deal with this number of individual molecules, but fortunately we don't have to. As long as we can study a big enough sample of them, our predictions of the properties of the bulk material should be reliable. The required sample size is often very large, but fortunately increasingly within the range that the most powerful modern-day computers can deal with. The aim of this project is to develop the software necessary to support these types of 'ensemble' calculations; software which will be very versatile and so theoretically able to applied to very many different areas of science.
Planned Impact
Who will benefit from this research:
In the commercial private sector computational modelling methods are applied in a wide range of areas concerned with complex and stochastic simulation, including the design and development of new medicines (not just drug design, but also formulation and delivery), the development of new catalysts, and the prediction of the properties of new materials. This research will allow workers in these fields to perform more rapid and more reliable calculations.
In manufacturing applications where precise control of materials is required e.g. control of thin film microstructure for the development of the next generation lithium ion batteries. This research could be adapted by workers in these fields to study, much more easily, more complex materials and to investigate, though much finer parameter sweeps, how they might be optimised.
In the public sector too there are potential beneficiaries - for example those using computer simulations to model the spread of epidemics, or to model the flow of pedestrians through a shopping centre, and how a safe evacuation could be assured. Workers in these fields could adapt the ExTASY tools to quickly evaluate large numbers of alternative scenarios, or use them in situations where parameters that influence the behaviour and fate of the model are not accurately known.
In the commercial private sector computational modelling methods are applied in a wide range of areas concerned with complex and stochastic simulation, including the design and development of new medicines (not just drug design, but also formulation and delivery), the development of new catalysts, and the prediction of the properties of new materials. This research will allow workers in these fields to perform more rapid and more reliable calculations.
In manufacturing applications where precise control of materials is required e.g. control of thin film microstructure for the development of the next generation lithium ion batteries. This research could be adapted by workers in these fields to study, much more easily, more complex materials and to investigate, though much finer parameter sweeps, how they might be optimised.
In the public sector too there are potential beneficiaries - for example those using computer simulations to model the spread of epidemics, or to model the flow of pedestrians through a shopping centre, and how a safe evacuation could be assured. Workers in these fields could adapt the ExTASY tools to quickly evaluate large numbers of alternative scenarios, or use them in situations where parameters that influence the behaviour and fate of the model are not accurately known.
Organisations
Publications
Ng HW
(2014)
Molecular dynamics simulations of the adenosine A2a receptor in POPC and POPE lipid bilayers: effects of membrane on protein behavior.
in Journal of chemical information and modeling
Ng HW
(2013)
Molecular dynamics simulations of the adenosine A2a receptor: structural stability, sampling, and convergence.
in Journal of chemical information and modeling
Pasi M
(2014)
µABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA.
in Nucleic acids research
Shkurti A
(2019)
CoCo-MD: A Simple and Effective Method for the Enhanced Sampling of Conformational Space.
in Journal of chemical theory and computation
Shkurti A
(2016)
pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data
in SoftwareX
Description | We have developed an integrated set of software tools that can be used by scientists who use computer simulations to study the structure and behaviour of biological molecules such as proteins. These tools make the computer simulations more efficient, so that the studies can be completed faster, and with less computer power. |
Exploitation Route | Elements of the software stack developed in this project have been further developed and refined in another current EPSRC funded project |
Sectors | Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology |
Description | EPSRC Flagship Software |
Amount | £523,963 (GBP) |
Funding ID | EP/P022138/1 |
Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
Sector | Public |
Country | United Kingdom |
Start | 06/2017 |
End | 11/2019 |
Description | EPSRC Project Grant |
Amount | £293,994 (GBP) |
Funding ID | EP/P011993/1 |
Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
Sector | Public |
Country | United Kingdom |
Start | 05/2017 |
End | 04/2020 |
Title | CoCo |
Description | CoCo is an enhanced sampling method for bimolecular simulation. |
Type Of Technology | Software |
Year Produced | 2015 |
Open Source License? | Yes |
Impact | Using CoCo, we have shown it is possible to sample conformational space more than an order of magnitude faster than using conventional MD. This has led to a new collaboration with a Pharmaceutical company and a grant application is currently in preparation. |
URL | https://bitbucket.org/extasy-project/coco |
Title | pyPcazip |
Description | Software for the efficient data-mining of large molecular dynamics simulation datasets |
Type Of Technology | Software |
Year Produced | 2014 |
Open Source License? | Yes |
Impact | The methodology has allowed us to test and maximise the reliability of predictions made from molecular dynamics simulations, and is now a standard protocol applied and discussed in all our MD-realted publications. |
URL | https://bitbucket.org/ramonbsc/pypcazip |
Description | CECAM workshop Juelich |
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 | An extended (two week), hands-on international workshop for early-career researchers to increase their understanding of, and promote their engagement with the latests developments in software for bimolecular simulation. There were 91 attendees from across Europe and the US. |
Year(s) Of Engagement Activity | 2015 |
URL | http://www.cecam.org/workshop-1214.html |
Description | Training workshop (Edinburgh) |
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 workshop provided training in the use of the ExTASY software for advanced sampling simulations in computational biology. However some of the participants came from outside the biological sciences - e.g. materials science. |
Year(s) Of Engagement Activity | 2016 |