Repositories list

• papers-and-grants

  Public
  YAML database of papers and grants from the Chodera lab

  Python

  •

  Creative Commons Zero v1.0 Universal

  •0•2•0•2•Updated Dec 25, 2024Dec 25, 2024

• machine_learned_potential_experiments

  Public
  Perform experiments with modelforge

  Shell

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  MIT License

  •0•0•0•0•Updated Dec 20, 2024Dec 20, 2024

• 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 Dec 13, 2024Dec 13, 2024

• pale

  Public
  The PALE: The Protein Alchemical Landscape Explorer

  Python

  •

  MIT License

  •1•2•1•0•Updated Dec 10, 2024Dec 10, 2024

• modelforge

  Public
  Infrastructure to implement and train NNPs

  Python

  •

  MIT License

  •5•12•19•6•Updated Dec 5, 2024Dec 5, 2024

• harbor

  Public
  A home for docking evaluation and assessment

  Python

  •

  MIT License

  •0•2•1•1•Updated Dec 5, 2024Dec 5, 2024

• 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•1•0•1•Updated Dec 5, 2024Dec 5, 2024

• fluorescence-assay

  Public
  Python

  •

  MIT License

  •0•0•0•1•Updated Dec 4, 2024Dec 4, 2024

• perses

  Public
  Experiments with expanded ensembles to explore chemical space

  molecular-dynamicsopenmmmolecular-design+ 5free-energy-perturbationrelative-free-energypythonsimulationexpanded-ensembles

  Python

  •

  MIT License

  •50•183•222•6•Updated Nov 26, 2024Nov 26, 2024

• avoidome-analysis

  Public
  A repository for downloading and analyzing the available Avoidome structures

  Jupyter Notebook

  •

  MIT License

  •1•3•1•0•Updated Nov 22, 2024Nov 22, 2024

• 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 for a set of related proteins

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Nov 20, 2024Nov 20, 2024

• espaloma

  Public
  Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196

  graph-learningforcefield-parameterization

  Python

  •

  MIT License

  •26•218•52•12•Updated Nov 18, 2024Nov 18, 2024

• openmmtools

  Public
  A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.

  molecular-dynamicsmcmcmarkov-chain-monte-carlo+ 7alchemical-free-energy-calculationsreplica-exchangeintegratorspythonopenmmmolecular-simulationsfree-energy-calculations

  Python

  •

  MIT License

  •80•256•221•26•Updated Nov 18, 2024Nov 18, 2024

• mtenn

  Public
  Modular Training and Evaluation of Neural Networks

  Python

  •

  MIT License

  •1•6•5•3•Updated Oct 10, 2024Oct 10, 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

• ffsettings

  Public
  Python

  •

  MIT License

  •0•0•0•1•Updated Oct 7, 2024Oct 7, 2024

• pymbar

  Public
  Python implementation of the multistate Bennett acceptance ratio (MBAR)

  researchpymbarequilibrium+ 9molecular-dynamics-simulationssingle-molecule-pullingmultistate-bennett-acceptance-ratiobennett-acceptance-ratioextended-bridge-samplingpythonfree-energies+ 2

  Python

  •

  MIT License

  •92•240•115•10•Updated Sep 30, 2024Sep 30, 2024

• 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•0•0•0•Updated Sep 12, 2024Sep 12, 2024

• drug-gym

  Public
  Reinforcement learning environments for drug discovery

  reinforcement-learningdrug-discovery

  Jupyter Notebook

  •

  MIT License

  •2•17•0•1•Updated Aug 23, 2024Aug 23, 2024

• evo-plr

  Public
  0•0•0•0•Updated Aug 16, 2024Aug 16, 2024

• espaloma-charge

  Public
  Standalone charge assignment from Espaloma framework.

  Python

  •

  MIT License

  •5•38•14•2•Updated Jul 12, 2024Jul 12, 2024

• folding_at_home_scripts

  Public
  This repository contains my scripts and notebooks to handle folding@home data

  Jupyter Notebook

  •

  MIT License

  •2•0•1•0•Updated May 22, 2024May 22, 2024

• refit-espaloma

  Public
  Refit espaloma with energies and forces

  Python

  •3•8•2•0•Updated May 16, 2024May 16, 2024

• nnp_testground

  Public
  MIT License

  •0•0•0•0•Updated May 2, 2024May 2, 2024

• espfit-experiment

  Public
  Workspace for espfit

  Python

  •1•1•0•0•Updated Apr 16, 2024Apr 16, 2024

• rna-benchmark

  Public
  RNA benchmarks associated with input coordinate files and experimental data

  Shell

  •0•0•0•0•Updated Apr 13, 2024Apr 13, 2024

• rna-espaloma

  Public
  Explore RNA systems with espaloma force field

  Jupyter Notebook

  •1•1•0•0•Updated Apr 13, 2024Apr 13, 2024

• asapdiscovery-ml-eval

  Public
  Tools for retrospective and propsective evaluation of ASAP ML models

  Python

  •

  MIT License

  •0•0•0•0•Updated Apr 12, 2024Apr 12, 2024

• espfit

  Public
  Refit espaloma with quantum chemical data and condensed phase properties of RNA systems

  Python

  •

  MIT License

  •0•1•6•1•Updated Apr 7, 2024Apr 7, 2024

• command-center

  Public
  Home of the ChoderaLab status monitor

  HTML

  •4•0•4•3•Updated Mar 25, 2024Mar 25, 2024