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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 240 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

    262 79

  5. openmmtools openmmtools Public

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

    Python 255 80

  6. status status Public

    3

Repositories

Showing 10 of 273 repositories
  • pale Public

    The PALE: The Protein Alchemical Landscape Explorer

    choderalab/pale’s past year of commit activity
    Python 2 MIT 1 1 0 Updated Dec 10, 2024
  • modelforge Public

    Infrastructure to implement and train NNPs

    choderalab/modelforge’s past year of commit activity
    Python 12 MIT 5 17 5 Updated Dec 5, 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 1 Updated Dec 5, 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 Dec 5, 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 Dec 5, 2024
  • missense-kinase-toolkit Public

    An 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 1 Updated Dec 5, 2024
  • fluorescence-assay Public
    choderalab/fluorescence-assay’s past year of commit activity
    Python 0 MIT 0 0 1 Updated Dec 4, 2024
  • perses Public

    Experiments with expanded ensembles to explore chemical space

    choderalab/perses’s past year of commit activity
    Python 182 MIT 50 222 (4 issues need help) 6 Updated Nov 26, 2024
  • avoidome-analysis Public

    A repository for downloading and analyzing the available Avoidome structures

    choderalab/avoidome-analysis’s past year of commit activity
    Jupyter Notebook 2 MIT 1 1 0 Updated Nov 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

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