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]

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

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

Name		Name	Last commit message	Last commit date
Latest commit History 372 Commits
2020-04-01-in-stock-and-one-step-synthesis		2020-04-01-in-stock-and-one-step-synthesis
SARS-CoV-inhibitors		SARS-CoV-inhibitors
anl		anl
covalent-docking		covalent-docking
fah-xray		fah-xray
folding-at-home_submissions		folding-at-home_submissions
london-libraries		london-libraries
melatonin		melatonin
molecules		molecules
moonshot-submissions		moonshot-submissions
redock-fragments		redock-fragments
repurposing-screen		repurposing-screen
roc-curve		roc-curve
scripts		scripts
synthetic-enumeration		synthetic-enumeration
.gitignore		.gitignore
LICENSE		LICENSE
README.md		README.md
environment.yml		environment.yml