(Complete) Protein-Ligand Benchmarks Automation via Folding@Home
- David Dotson
- Jeffrey Wagner
- Diego Nolasco (Deactivated)
Primary Driver | @David Dotson |
Approvers | (OpenFF) (Chodera Lab, and F@H, and ASAP) (OpenFE) Project approvers agreed to dissolve as goals were completed on 2023_10_30 |
Supporting Drivers | @Lorenzo D'Amore |
Stakeholders | @Simon Boothroyd Irfan Alibay @Richard Gowers David Swenson @Jeffry Setiadi @Lorenzo D'Amore @Lily Wang Antonia Mey @David Mobley
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Project Manager |
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Decision authority | Unanimity of Primary Driver and two Approvers (absences are vetos), only in synchronous meetings Veto authority: Primary Driver, any Approver |
Discussion/ Notification Venue | Weekly meetings (decision forum) #free-energy-benchmarking channel on OpenFF slack (notification and discussion, no major decisions allowed here)
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Objective | Leverage Folding@Home for automated, continuous benchmarking of new generations of OpenFF forcefields via binding free energy calculations for a library of protein-ligand systems. |
Due date | Oct 1, 2022 |
Status | Complete |
Problem Statement
Thus far in the project, protein-ligand benchmarks for OpenFF have been a manual process performed on Janssen cluster resources. As new generations of OpenFF forcefields are released, the burden of executing free energy calculations to assess improvement and deficiency will increase, as will the computational cost.
We would like to improve this situation by:
Leveraging the immense computational resources provided by Folding@Home for near-continuous free energy benchmarking of new force fields against a library of protein-ligand systems.
Introducing automation that minimizes human-in-the-loop requirements for this benchmarking into the future.
Executing free energy calculations via both Gromacs and OpenMM.
Current project specification
(The link below should be considered an authoritative source of truth for this project at the moment. This may be updated in the future)
Milestones and deadlines
Milestone | Deadline | Status | Completion |
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Working group recruitment “Read the google doc, provide use cases in the form of “I expect to put X in as an input, and get Y out as an output. State availability for weekly meetings starting as early as Feb 8” | Feb 4 2022 | COMPLETE | @David Dotson @Diego Nolasco (Deactivated) |
First meeting - How project is managed, open discussion of use cases | Feb 15 2022 | COMPLETE |
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Second meeting - Further refinement of use cases | Feb 22 2022 | COMPLETE |
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Scope/use case review | Mar 8 2022 | complete | @David Dotson @John Chodera @Jeffrey Wagner |
Initial API defined (example notebook or command block for each user story?) | 2022.09.15 | COMPLETE |
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alchemiscale release 0.1.0 | 2022.09.15 | complete | 2023.04.17 |
protein-ligand-benchmark release 0.3.0 | 2022.09.15 | IN progress |
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“MVP” - Core infrastructure stand-up as development environment to enable rapid iteration, involvement of stakeholders | 2022.09.15 | COMPLETE | 2023.04.21 @David Dotson @John Chodera @Jeffrey Wagner |
Software development, integration and testing cycles | 2022.09.15 | complete | @David Dotson @John Chodera @Jeffrey Wagner |
Production environment stand-up and deployment; ideally using promotion mechanism from a QA environment | 2022.10.01 | COMPLETE | 2023.04.23 @David Dotson @John Chodera @Jeffrey Wagner @David Dotson @John Chodera @Jeffrey Wagner |
Reference materials
https://docs.google.com/document/d/1wcTy4TqBIGbxdt9p2reVTY4J5iKAzF673DQsZeZ8vg8/edit?pli=1#
https://drive.google.com/file/d/1_N3yFBRKU8HoE4XCSfPrY26UFlncVGA8/view?pli=1
https://drive.google.com/file/d/1XRpJ9OELd005BCZRn7uwEpMqu70_f8yh/view