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    282 repositories

    • payne2025how_code

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Apr 25, 2026Apr 25, 2026

    • mtenn

      Public
      Modular Training and Evaluation of Neural Networks
      Python
      •
      MIT License
      •2•8•9•3•Updated Apr 22, 2026Apr 22, 2026

    • drugforge

      Public
      Toolkit for open antiviral drug discovery by the Choderalab (formerly ASAP)
      Python
      •
      MIT License
      •1•11•45•9•Updated Apr 21, 2026Apr 21, 2026

    • modelforge

      Public
      Infrastructure to implement and train NNPs
      Python
      •
      MIT License
      •5•24•16•6•Updated Apr 20, 2026Apr 20, 2026

    • choderalab.github.io

      Public
      The ChoderaLab website
      HTML
      •
      MIT License
      •1•0•14•2•Updated Apr 20, 2026Apr 20, 2026

    • espaloma

      Public
      Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196
      graph-learningforcefield-parameterization
      graph-learningforcefield-parameterization
      Python
      •
      MIT License
      •30•270•53•9•Updated Apr 16, 2026Apr 16, 2026

    • harbor

      Public
      A home for docking evaluation and assessment
      Python
      •
      MIT License
      •0•2•3•2•Updated Apr 9, 2026Apr 9, 2026

    • missense-kinase-toolkit

      Public
      A package to facilitate structure- and sequence-based ML for clinically relevant missense human kinase property prediction
      Python
      •
      MIT License
      •0•3•0•3•Updated Apr 6, 2026Apr 6, 2026

    • asapdiscovery-sars-retrospective

      Public
      Repository to store the code used for a paper exploring methods for SARS-2 Mpro Docking.
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •0•0•1•1•Updated Mar 24, 2026Mar 24, 2026

    • slc33a1_md

      Public
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Mar 13, 2026Mar 13, 2026

    • ip3r_md

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 11, 2026Mar 11, 2026

    • pymbar

      Public
      Python implementation of the multistate Bennett acceptance ratio (MBAR)
      pythonresearchpymbar
      pythonresearchpymbarfree-energiesthermodynamic-statesequilibriummolecular-dynamics-simulationssingle-molecule-pullingmbarmultistate-bennett-acceptance-ratio
      Python
      •
      MIT License
      •99•297•126•11•Updated Feb 12, 2026Feb 12, 2026

    • papers-and-grants

      Public
      YAML database of papers and grants from the Chodera lab
      Python
      •
      Creative Commons Zero v1.0 Universal
      •0•2•0•1•Updated Jan 28, 2026Jan 28, 2026

    • how-to-get-a-job

      Public
      Talk slides on how to get a job
      HTML
      •
      Creative Commons Zero v1.0 Universal
      •0•1•0•0•Updated Jan 28, 2026Jan 28, 2026

    • openmmtools

      Public
      A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
      pythonmolecular-dynamicsopenmm
      pythonmolecular-dynamicsopenmmmolecular-simulationsmcmcmarkov-chain-monte-carloalchemical-free-energy-calculationsfree-energy-calculationsreplica-exchangeintegrators
      Python
      •
      MIT License
      •86•319•232•26•Updated Jan 7, 2026Jan 7, 2026

    • pale

      Public
      The PALE: The Protein Alchemical Landscape Explorer
      Jupyter Notebook
      •
      MIT License
      •2•3•2•2•Updated Nov 18, 2025Nov 18, 2025

    • perses

      Public
      Experiments with expanded ensembles to explore chemical space
      pythonsimulationmolecular-dynamics
      pythonsimulationmolecular-dynamicsopenmmmolecular-designfree-energy-perturbationexpanded-ensemblesrelative-free-energy
      Python
      •
      MIT License
      •50•199•224•7•Updated Oct 28, 2025Oct 28, 2025

    • espaloma-charge

      Public
      Standalone charge assignment from Espaloma framework.
      Python
      •
      MIT License
      •7•47•20•4•Updated Oct 10, 2025Oct 10, 2025

    • ffsettings

      Public
      Python
      •
      MIT License
      •0•0•0•1•Updated Oct 6, 2025Oct 6, 2025

    • fluorescence-assay

      Public
      Python
      •
      MIT License
      •0•0•0•5•Updated Oct 6, 2025Oct 6, 2025

    • broad-spectrum-asap-paper

      Public
      Scripts and input files for structure-based prediction of affinity across the coronavirus family.
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Aug 2, 2025Aug 2, 2025

    • fragment-fold

      Public
      The goal of this repository is to house the scripts and data for taking a fragment screen from the Diamond Light Source and generating a modeled fragment screen…
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jun 23, 2025Jun 23, 2025

    • knowledge-base

      Public
      A repository for Chodera Lab members to get up to speed on the foundational knowledge necessary for getting the most out of the lab!
      TeX
      •
      MIT License
      •0•4•1•0•Updated Apr 21, 2025Apr 21, 2025

    • machine_learned_potential_experiments

      Public
      Perform experiments with modelforge
      Shell
      •
      MIT License
      •0•2•0•0•Updated Feb 5, 2025Feb 5, 2025

    • status

      Public
      0•3•2•1•Updated Jan 31, 2025Jan 31, 2025

    • kinfold

      Public
      Modified AlphaFold 2 with a focus on templating for multi-state kinase predictions.
      Python
      •
      Apache License 2.0
      •2.6k•0•0•0•Updated Jan 29, 2025Jan 29, 2025

    • timemachine_hydration_paper

      Public
      Differentiate all the things!
      Python
      •
      Other
      •19•2•0•2•Updated Jan 12, 2025Jan 12, 2025

    • avoidome-analysis

      Public
      A repository for downloading and analyzing the available Avoidome structures
      Jupyter Notebook
      •
      MIT License
      •1•6•1•0•Updated Nov 22, 2024Nov 22, 2024

    • fah-db

      Public
      This repo is meant to be a lightweight way to manage the input files for F@h.
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 7, 2024Oct 7, 2024

    • drug-gym

      Public
      Reinforcement learning environments for drug discovery
      reinforcement-learningdrug-discovery
      reinforcement-learningdrug-discovery
      Jupyter Notebook
      •
      MIT License
      •2•18•0•1•Updated Aug 23, 2024Aug 23, 2024
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