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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 242 92

  2. yank yank Public

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

    Python 181 71

  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

    263 79

  5. openmmtools openmmtools Public

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

    Python 257 81

  6. status status Public

    3

Repositories

Showing 10 of 274 repositories
  • perses Public

    Experiments with expanded ensembles to explore chemical space

    choderalab/perses’s past year of commit activity
    Python 184 MIT 50 222 (4 issues need help) 7 Updated Jan 15, 2025
  • openmmtools Public

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

    choderalab/openmmtools’s past year of commit activity
    Python 257 MIT 81 221 27 Updated Jan 15, 2025
  • 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 1 Updated Jan 14, 2025
  • modelforge Public

    Infrastructure to implement and train NNPs

    choderalab/modelforge’s past year of commit activity
    Python 13 MIT 5 19 8 Updated Jan 13, 2025
  • timemachine_hydration_paper Public Forked from proteneer/timemachine

    Differentiate all the things!

    choderalab/timemachine_hydration_paper’s past year of commit activity
    Python 0 17 0 2 Updated Jan 12, 2025
  • papers-and-grants Public

    YAML database of papers and grants from the Chodera lab

    choderalab/papers-and-grants’s past year of commit activity
    Python 2 CC0-1.0 0 0 2 Updated Jan 11, 2025
  • choderalab/fluorescence-assay’s past year of commit activity
    Python 0 MIT 0 0 3 Updated Jan 6, 2025
  • ffsettings Public
    choderalab/ffsettings’s past year of commit activity
    Python 0 MIT 0 0 1 Updated Jan 6, 2025
  • missense-kinase-toolkit Public

    A package to facilitate structure- and sequence-based ML for clinically relevant missense human kinase property prediction

    choderalab/missense-kinase-toolkit’s past year of commit activity
    Python 1 MIT 0 0 2 Updated Jan 6, 2025
  • 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 Dec 20, 2024

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