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@choderalab

Chodera lab // Memorial Sloan Kettering Cancer Center

Pinned

  1. pymbar pymbar Public

    Python implementation of the multistate Bennett acceptance ratio (MBAR)

    Python 219 89

  2. yank yank Public

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

    Python 171 69

  3. assaytools assaytools Public

    Modeling and Bayesian analysis of fluorescence and absorbance assays.

    Python 17 11

  4. software-development software-development Public

    A primer on software development best practices for computational chemistry

    251 76

  5. openmmtools openmmtools Public

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

    Python 234 75

  6. status status Public

    3

Repositories

Showing 10 of 269 repositories
  • drug-gym Public

    Reinforcement learning environments for drug discovery

    Jupyter Notebook 9 MIT 1 0 0 Updated Apr 29, 2024
  • asapdiscovery Public

    Toolkit for open antiviral drug discovery by the ASAP Discovery Consortium

    Python 20 MIT 1 165 (2 issues need help) 18 Updated Apr 29, 2024
  • harbor Public

    A home for docking evaluation and assessment

    Python 2 MIT 0 0 1 Updated Apr 27, 2024
  • modelforge Public

    Infrastructure to implement and train NNPs

    Python 8 MIT 3 9 8 Updated Apr 27, 2024
  • openmmtools Public

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

    Python 234 MIT 75 199 27 Updated Apr 26, 2024
  • espaloma_charge Public

    Standalone charge assignment from Espaloma framework.

    Python 32 MIT 5 12 3 Updated Apr 25, 2024
  • asapdiscovery-sars-retrospective Public

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

    Jupyter Notebook 0 CC0-1.0 0 1 0 Updated Apr 25, 2024
  • feflow Public

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

    Python 9 MIT 1 22 7 Updated Apr 22, 2024
  • mtenn Public

    Modular Training and Evaluation of Neural Networks

    Python 5 MIT 1 4 2 Updated Apr 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 0 MIT 0 0 0 Updated Apr 19, 2024

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