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Python implementation of the multistate Bennett acceptance ratio (MBAR)
Automated omics-scale protein modeling and simulation setup.
An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
Modeling and Bayesian analysis of fluorescence and absorbance assays.
A primer on software development best practices for computational chemistry
An OpenMM toolkit with test systems, integrators, and alchemical support
Recurrent Units-based Molecular Modeling
Evaluating MSM-estimated mean first passage times
Experiments with expanded ensembles to explore chemical space
OpenMM testbed for constant-pH methodologies.
SAMPL6 physicochemical property prediction challenge (logD, pKa and solubility)
Standard experimental accuracy benchmark set for YANK.
Material for our first kinase inhibitor fluorescence assay paper.
An open set of tools for automating tasks relating to small molecules
Latex manuscript for the SAMPL6 epik and jaguar pKa paper
A tool for modeling different kinase conformations with various ligand binding poses.
Code and data for the paper 'What makes a kinase promiscuous for inhibitors?'.
Bayesian statistics-based assay modelling, accelerated by TensorFlow.
Records of ITC Experiments
Open source toolkit for predicting bacterial porin permeation
Repository for SAMPL6 pKa measurements manuscript.
A collection of protocols, primarily for automated protein expression and mutagenesis
Examples for use of YANK - getyank.org
Utilities to run on MPI.
Attempted implementation of Frank Noe's summer students's work on observable tICA
Bacterial porin permeation calculation examples for iapetus
Titrato (name pending) is a set of tools for analyzing pKa data.
Examples for MHC-peptide free energy calculations using YANK
Reference pKa calculations for the SAMPL6 pKa challenge
Examples for fragmenter