Grow your team on GitHub
GitHub is home to over 28 million developers working together. Join them to grow your own development teams, manage permissions, and collaborate on projects.Sign up
An OpenMM toolkit with test systems, integrators, and alchemical support
Investigating the error introduced by neglecting shadow work
Python-centric Cookiecutter for Molecular Computational Chemistry Packages
Attempted implementation of Frank Noe's summer students's work on observable tICA
A collection of protocols, primarily for automated protein expression and mutagenesis
An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
Selection of kinase constructs suitable for E coli expression
Experiments with expanded ensembles to explore chemical space
Repository for SAMPL6 pKa measurements manuscript.
Examples for use of YANK - getyank.org
Evaluating MSM-estimated mean first passage times
A primer on software development best practices for computational chemistry
Investigation into the effect of shadow work on nonequilibrium switching based relative free energy calculations
Tools for Munging Folding@Home datasets
OpenMM testbed for constant-pH methodologies.
Examples for fragmenter
Experiments in adaptive sampling with trpzip2  as a model system
Standard experimental accuracy benchmark set for YANK.
Reference pKa calculations for the SAMPL6 pKa challenge
a collection of scripts and files to help in PDB retrieval for various projects
Titrato (name pending) is a set of tools for analyzing pKa data.
Latex manuscript for the SAMPL6 epik and jaguar pKa paper
Open source toolkit for predicting bacterial porin permeation
Bacterial porin permeation calculation examples for iapetus
Change Point detection
SAMPL6 physicochemical property prediction challenge (logD, pKa and solubility)
Cheminformatic analysis of small molecule type drugs in DrugBank for their ability to form nanoparticles with indocyanine dyes.