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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 224 89

  2. yank yank Public

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

    Python 172 69

  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

    254 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 10 7 Updated Jun 20, 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 20, 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 24 6 Updated Jun 19, 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 Jun 18, 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
  • harbor Public

    A home for docking evaluation and assessment

    choderalab/harbor’s past year of commit activity
    Python 2 MIT 0 1 1 Updated Jun 7, 2024
  • mtenn Public

    Modular Training and Evaluation of Neural Networks

    choderalab/mtenn’s past year of commit activity
    Python 5 MIT 1 5 2 Updated Jun 6, 2024
  • drug-gym Public

    Reinforcement learning environments for drug discovery

    choderalab/drug-gym’s past year of commit activity
    Jupyter Notebook 12 MIT 1 0 0 Updated May 23, 2024
  • folding_at_home_scripts Public Forked from sperezconesa/folding_at_home_scripts

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

    choderalab/folding_at_home_scripts’s past year of commit activity
    Jupyter Notebook 0 MIT 2 1 0 Updated May 22, 2024
  • refit-espaloma Public

    Refit espaloma with energies and forces

    choderalab/refit-espaloma’s past year of commit activity
    Python 6 2 2 0 Updated May 16, 2024
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