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@choderalab

Chodera lab // Memorial Sloan Kettering Cancer Center

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  1. pymbar pymbar Public

    Python implementation of the multistate Bennett acceptance ratio (MBAR)

    Python 228 89

  2. yank yank Public

    An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.

    Python 175 70

  3. assaytools assaytools Public

    Modeling and Bayesian analysis of fluorescence and absorbance assays.

    Python 18 11

  4. software-development software-development Public

    A primer on software development best practices for computational chemistry

    255 76

  5. openmmtools openmmtools Public

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

    Python 236 76

  6. status status Public

    3

Repositories

Showing 10 of 270 repositories
  • modelforge Public

    Infrastructure to implement and train NNPs

    choderalab/modelforge’s past year of commit activity
    Python 9 MIT 4 14 12 Updated Jul 15, 2024
  • feflow Public

    Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits

    choderalab/feflow’s past year of commit activity
    Python 10 MIT 1 25 6 Updated Jul 12, 2024
  • espaloma_charge Public

    Standalone charge assignment from Espaloma framework.

    choderalab/espaloma_charge’s past year of commit activity
    Python 35 MIT 5 14 2 Updated Jul 12, 2024
  • mtenn Public

    Modular Training and Evaluation of Neural Networks

    choderalab/mtenn’s past year of commit activity
    Python 5 MIT 1 4 2 Updated Jul 12, 2024
  • drug-gym Public

    Reinforcement learning environments for drug discovery

    choderalab/drug-gym’s past year of commit activity
    Jupyter Notebook 13 MIT 1 0 0 Updated Jul 9, 2024
  • openmmtools Public

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

    choderalab/openmmtools’s past year of commit activity
    Python 236 MIT 76 204 28 Updated Jul 4, 2024
  • missense-kinase-toolkit Public

    An ETL pipeline package to facilitate structure-based ML for missense human kinase property prediction

    choderalab/missense-kinase-toolkit’s past year of commit activity
    Python 1 MIT 0 0 0 Updated Jul 1, 2024
  • ffsettings Public
    choderalab/ffsettings’s past year of commit activity
    Python 0 MIT 0 0 1 Updated Jul 1, 2024
  • machine_learned_potential_experiments Public

    Perform experiments with modelforge

    choderalab/machine_learned_potential_experiments’s past year of commit activity
    Shell 0 MIT 0 0 0 Updated Jun 29, 2024
  • asapdiscovery-sars-retrospective Public

    Repository to store the code used for a paper exploring methods for SARS-2 Mpro Docking.

    choderalab/asapdiscovery-sars-retrospective’s past year of commit activity
    Jupyter Notebook 0 CC0-1.0 0 1 0 Updated Jun 7, 2024
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