CCP-BioSim: Biomolecular simulation at the life sciences interface
Lead Research Organisation:
University of Southampton
Department Name: Sch of Chemistry
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
People |
ORCID iD |
| Jonathan Essex (Principal Investigator) |
Publications
Aldeghi M
(2018)
Large-scale analysis of water stability in bromodomain binding pockets with grand canonical Monte Carlo.
in Communications chemistry
Bruce Macdonald HE
(2018)
Ligand Binding Free Energies with Adaptive Water Networks: Two-Dimensional Grand Canonical Alchemical Perturbations.
in Journal of chemical theory and computation
Ekberg V
(2022)
Comparison of Grand Canonical and Conventional Molecular Dynamics Simulation Methods for Protein-Bound Water Networks.
in ACS physical chemistry Au
Ge Y
(2022)
Enhancing Sampling of Water Rehydration on Ligand Binding: A Comparison of Techniques.
in Journal of chemical theory and computation
H. Bruce Macdonald
(2018)
Predicting water networks and ligand binding free energies using grand canonical Monte Carlo
Huggins D
(2018)
Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity
in WIREs Computational Molecular Science
| Description | This grant supported a range of networking activities for the biomolecular simulation community in the UK. These included the provision of training workshops and conferences. These objectives were met. In addition there was a research component looking to develop simulation methods for biomolecular modelling, and in particular multiscale approaches. As part of this activity we have developed a new simulation approach to explore and quantify water binding in protein-ligand systems. There is considerable interest in this work from academic and industrial partners. We have deployed these methods in the latest version of our simulation code, and we are providing training workshops to academia and industry to facilitate take up of these methods. |
| Exploitation Route | The CCP has been renewed so further community activities are taking place. The research outputs are being further developed and tested by members of my research team. Discussions with other partners regarding the use of these research outputs are in progress. |
| Sectors | Pharmaceuticals and Medical Biotechnology |
| URL | http://www.essexgroup.soton.ac.uk/ProtoMS/index.html |
| Description | The training workshops supported by this grant have disseminated modern, sophisticated computer simulation methods into industry. The software is now being implemented as part of industry work-flows. |
| First Year Of Impact | 2019 |
| Sector | Pharmaceuticals and Medical Biotechnology |
| Impact Types | Economic |
| Description | High-End Computing Consortia |
| Amount | £288,481 (GBP) |
| Funding ID | EP/L000253/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2013 |
| End | 10/2018 |
| Description | RS Newton Fellowship |
| Amount | £99,000 (GBP) |
| Funding ID | NF171278 |
| Organisation | The Royal Society |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 03/2018 |
| End | 02/2020 |
| Description | collaboration with UC Irvine |
| Organisation | University of California, Irvine |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | we have applied the methods developed under this grant to a joint publication |
| Collaborator Contribution | they provided alternative simulation methods against which we were able to make a comparison |
| Impact | one publication |
| Start Year | 2021 |
| Description | collaboration with University of Athens |
| Organisation | National and Kapodistrian University of Athens |
| Department | Neurology Athens |
| Country | Greece |
| Sector | Academic/University |
| PI Contribution | provision of novel simulation methodology |
| Collaborator Contribution | provision of experimental data |
| Impact | one publication |
| Start Year | 2020 |
| Description | collaboration with Uppsala University |
| Organisation | Uppsala University |
| Country | Sweden |
| Sector | Academic/University |
| PI Contribution | provision of novel simulation methodology |
| Collaborator Contribution | provision of alternative simulation approach |
| Impact | one publication |
| Start Year | 2020 |
| Description | water network analysis |
| Organisation | University of Oxford |
| Department | Department of Biochemistry |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Training and insights related to our methods. |
| Collaborator Contribution | Partners provided the data and and associated collaborators for us to use in our analysis. |
| Impact | Paper reporting collaboration results published, |
| Start Year | 2016 |
| Title | Grand - an OpenMM module for grand canonical Monte Carlo |
| Description | This software allows grand canonical Monte Carlo calculations to be performed in the OpenMM simulation environment |
| Type Of Technology | Software |
| Year Produced | 2020 |
| Open Source License? | Yes |
| Impact | None yet |
| Title | ProtoCaller |
| Description | Software to automate the setup of free energy calculations |
| Type Of Technology | Software |
| Year Produced | 2020 |
| Open Source License? | Yes |
| Impact | non yet |
| URL | https://protocaller.readthedocs.io/en/latest/index.html |
| Title | ProtoMS 3.0 |
| Description | This is a Monte Carlo biomolecular simulation program which has been written and developed by members of my research group over a number of years. The latest release version, 3.0, was co-written in part by the postdoc currently employed under this grant. |
| Type Of Technology | Software |
| Year Produced | 2014 |
| Open Source License? | Yes |
| Impact | A CCPBioSim training workshop using this new version of the software will take place on November 25th 2014 at the University of Southampton. Academic and industrial users will attend from the UK. |
| Title | ProtoMS 3.2 |
| Description | This software allows for the calculation of protein-ligand binding free energies. This most recent version incorporates our latest work on grand canonical Monte Carlo. |
| Type Of Technology | Software |
| Year Produced | 2015 |
| Open Source License? | Yes |
| Impact | This software is being adopted by other academics and some industrial partners are also using it. |
| URL | http://www.essexgroup.soton.ac.uk/ProtoMS/ |
| Title | ProtoMS 3.3 |
| Description | This software allows the user to perform protein-ligand binding free energy calculations using advanced Monte Carlo methods, including grand canonical Monte Carlo. |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | This software is currently being deployed to industrial collaborators. Its impact in this context will be assessed once these deployments are complete. |
| URL | http://www.essexgroup.soton.ac.uk/ProtoMS/index.html |
| Description | Industry training workshops |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Training on our software ProtoMS was given to three industrial partners - GSK, AZ and UCB. This involved visits to the industrial sites, presentation of the theory underpinning the work, and the provision of training materials. |
| Year(s) Of Engagement Activity | 2017 |