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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 235 91

  2. yank yank Public

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

    Python 177 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

    260 77

  5. openmmtools openmmtools Public

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

    Python 244 76

  6. status status Public

    3

Repositories

Showing 10 of 271 repositories
  • 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!

    choderalab/knowledge-base’s past year of commit activity
    TeX 0 MIT 0 0 0 Updated Sep 12, 2024
  • modelforge Public

    Infrastructure to implement and train NNPs

    choderalab/modelforge’s past year of commit activity
    Python 11 MIT 4 13 9 Updated Sep 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 Sep 11, 2024
  • openmmtools Public

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

    choderalab/openmmtools’s past year of commit activity
    Python 244 MIT 76 210 30 Updated Sep 10, 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 Sep 5, 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 1 Updated Sep 3, 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 13 MIT 1 27 5 Updated Aug 29, 2024
  • pymbar Public

    Python implementation of the multistate Bennett acceptance ratio (MBAR)

    choderalab/pymbar’s past year of commit activity
    Python 235 MIT 91 111 10 Updated Aug 28, 2024
  • drug-gym Public

    Reinforcement learning environments for drug discovery

    choderalab/drug-gym’s past year of commit activity
    Jupyter Notebook 14 MIT 1 0 0 Updated Aug 23, 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

    choderalab/fragment-fold’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Aug 20, 2024
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