Chodera lab // Memorial Sloan Kettering Cancer Center

openmmtools

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

pymbar

Python implementation of the multistate Bennett acceptance ratio (MBAR)

espaloma

Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196

perses

Experiments with expanded ensembles to explore chemical space

espaloma_charge

Standalone charge assignment from Espaloma framework.

asapdiscovery

Toolkit for open antiviral drug discovery by the ASAP Discovery Consortium

chiron

Differentiable Markov Chain Monte Carlo

perses-barnase-barstar-paper

Contains scripts and data for the perses barnase barstar paper

drug-gym

Reinforcement learning environments for drug discovery

feflow

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

modelforge

Infrastructure to implement and train NNPs

mtenn

Modular Training and Evaluation of Neural Networks

status

harbor

A home for docking evaluation and assessment

avoidome-analysis

A repository for downloading and analyzing the available Avoidome structures

missense-kinase-toolkit

An ETL pipeline package to facilitate structure-based ML for missense human kinase property prediction

rna-espaloma

Explore RNA systems with espaloma force field

asapdiscovery-sars-retrospective

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

command-center

Home of the ChoderaLab status monitor

fragment-fold

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

asapdiscovery-ml-eval

Tools for retrospective and propsective evaluation of ASAP ML models

espfit

Refit espaloma with quantum chemical data and condensed phase properties of RNA systems

espfit-experiment

Workspace for espfit

ffsettings

knowledge-base

A repository for Chodera Lab members to get up to speed on the foundational knowledge necessary for getting the most out of the lab!

nnp_testground

pl-benchmark-espaloma-experiment

Alchemical protein-ligand benchmark experiment using Perses and espaloma force field

rbd-ace2-xbb15-simulations

rna-benchmark

RNA benchmarks associated with input coordinate files and experimental data

vanilla-espaloma-experiment

Vanilla MD simulation of protein-ligand complex using espaloma-0.3