Chodera lab // Memorial Sloan Kettering Cancer Center

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Memorial Sloan-Kettering Cancer Center, Manhattan, NY
http://choderalab.org
john.chodera@choderalab.org

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pymbarpymbarPublic
Python implementation of the multistate Bennett acceptance ratio (MBAR)
Python 246 93
software-developmentsoftware-developmentPublic
A primer on software development best practices for computational chemistry
263 79
openmmtoolsopenmmtoolsPublic
A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
Python 263 84
modelforgemodelforgePublic
Infrastructure to implement and train NNPs
Python 13 5
espalomaespalomaPublic
Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196
Python 229 27
mtennmtennPublic
Modular Training and Evaluation of Neural Networks
Python 6 1

Repositories

Showing 10 of 277 repositories

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 1MIT0 0 2 UpdatedMar 15, 2025
harbor Public
A home for docking evaluation and assessment
choderalab/harbor’s past year of commit activity
Python 2MIT0 1 2 UpdatedMar 14, 2025
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 Notebook0MIT0 0 0 UpdatedMar 14, 2025
modelforge Public
Infrastructure to implement and train NNPs
choderalab/modelforge’s past year of commit activity
Python 13MIT 5 14 6 UpdatedMar 14, 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 Notebook0CC0-1.00 1 0 UpdatedMar 13, 2025
mtenn Public
Modular Training and Evaluation of Neural Networks
choderalab/mtenn’s past year of commit activity
Python 6MIT 1 5 3 UpdatedMar 13, 2025
broad-spectrum-asap-paper Public
Scripts and input files for structure-based prediction of affinity across the coronavirus family.
choderalab/broad-spectrum-asap-paper’s past year of commit activity
Jupyter Notebook0CC0-1.00 0 0 UpdatedMar 11, 2025
asapdiscovery Public Forked fromasapdiscovery/asapdiscovery
Toolkit for open antiviral drug discovery by the ASAP Discovery Consortium
choderalab/asapdiscovery’s past year of commit activity
Python0MIT 2 0 0 UpdatedMar 10, 2025
fluorescence-assay Public
choderalab/fluorescence-assay’s past year of commit activity
Python0MIT0 0 5 UpdatedMar 7, 2025
pale Public
The PALE: The Protein Alchemical Landscape Explorer
choderalab/pale’s past year of commit activity
Python 2MIT 1 1 0 UpdatedFeb 24, 2025