README.md

Docking and free energy calculations for the COVID Moonshot

This repository contains all the scripts and output for docking and free energy calculations of COVID Moonshot submissions run on Folding@home.

Alchemical free energy calculation dashboards

• Sprint 4: [dashboard] [analysis.json](something is wrong with the dashboard, but the analysis.json works)
• Sprint 5: [dashboard] [analysis.json]
• Sprint 5 stereofix monomer neutral: [dashboard] [analysis.json]
• Sprint 5 stereofix dimer neutral: [dashboard] [analysis.json]
• Sprint 7: [dashboard] [analysis.json] Sprint 8 neutral restrained: [dashboard] [analysis.json]
• Sprint 9 neutral restrained: [dashboard] [analysis.json]
• Sprint 9 neutral unrestrained: [dashboard] [analysis.json]
• Sprint 10 restrained: [dashboard] [analysis.json]
• Sprint 10 unrestrained: [dashboard] [analysis.json]
• Sprint 11 neutral unrestrained: [dashboard] [analysis.json]
• Sprint 11 neutral restrained: [dashboard] [analysis.json]
• Sprint 11 charged unrestrained: [dashboard] [analysis.json]
• Sprint 11 charged restrained: [dashboard] [analysis.json]
• Sprint 11A neutral unrestrained: [dashboard] [analysis.json]
• Sprint 11A neutral restrained: [dashboard] [analysis.json]
• Sprint 11A charged unrestrained: [dashboard] [analysis.json]
• Sprint 11A charged restrained: [dashboard] [analysis.json]
• Sprint 12 charged dyad His163neutral: [dashboard] [analysis.json]
• Sprint 12 charged dyad His163charged: [dashboard] [analysis.json]

Contributors

• John D. Chodera (MSKCC) <[email protected]>
• Matt Hurley <Matt Hurley <[email protected]>
• Hannah Bruce Macdonald [email protected]
• William Glass [email protected]

Manifest

• diamond-structures/ - source structures of SARS-CoV-2 main viral protease from DiamondMX/XChem
• receptors/ - receptor structures prepared for docking and simulation by the OpenEye Spruce Toolkit
• scripts/ - scripts for preparing receptors, docking ligands, and setting up free energy calculations
• environment.yml - conda environment used for calculations
• moonshot-submissions/ - input files and docking results for submitted batches of COVID Moonshot compounds
• covalent-docking/ - input files and constrained docking results for subset of COVID Moonshot compounds with covalent warheads
• synthetic-enumeration/ - input scripts for alchemical free energy calculations on Folding@home

Outdated

• redock-fragments/ - generation of ROC to assess recovery of hits from missess in screened fragments
• 2020-04-01-in-stock-and-one-step-synthesis/ - docking of high-priority compounds for initial triage round
• melatonin/ - docking of melatonin and metabolites after observation that x0104 is extremely similar to melatonin
• simulation_prep/ - historical scripts and input files used in preparing gromacs expanded ensemble free energy calculations for Folding@home