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Open source toolkit for predicting bacterial porin permeation
Bacterial porin permeation calculation examples for iapetus
Experiments with expanded ensembles to explore chemical space
An OpenMM toolkit with test systems, integrators, and alchemical support
Utilities to run on MPI.
Modeling and Bayesian analysis of fluorescence and absorbance assays.
Records of ITC Experiments
Code and data for the paper 'What makes a kinase promiscuous for inhibitors?'.
Evaluating MSM-estimated mean first passage times
An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
OpenMM testbed for constant-pH methodologies.
SAMPL6 physicochemical property prediction challenge (logD, pKa and solubility)
A collection of protocols, primarily for automated protein expression and mutagenesis
Titrato (name pending) is a set of tools for analyzing pKa data.
Repository for SAMPL6 pKa measurements manuscript.
Examples for MHC-peptide free energy calculations using YANK
Reference pKa calculations for the SAMPL6 pKa challenge
Examples for fragmenter
Molecular simulation algorithms and computational statistics blog
Tools for setting up ITC experiments in an automated fashion using the Tecan EVO and Auto-iTC 200.
Validation input files for YANK
Standard experimental accuracy benchmark set for YANK.
Host-guest system data and simulations
CHARMM and AMBER forcefields for OpenMM
Examples for use of YANK - getyank.org
Latex manuscript for the SAMPL6 epik and jaguar pKa paper
A primer on software development best practices for computational chemistry