GITHUB
All our code is free and open source on GitHub!
Read (and contribute to!) our notes on Software Development Best Practices for Computational Chemistry.
OPENMM
We contribute to the development of the GPU-accelerated OpenMM molecular modeling package, one of the fastest platforms for molecular simulation.
Read the documentation at docs.openmm.org
Go to the Github page
Read the latest OpenMM paper
Get it via conda
OPENMMTOOLS
A useful library layer of high-quality integrators, a composable MCMC framework, advanced sampling schemes, alchemical factories, and test systems for OpenMM.
Read the documentation at openmmtools.readthedocs.io
Go to the GitHub page
PYMBAR
A Python implementation of the multistate Bennett acceptance ratio method.
Read the documentation at pymbar.org
Go to the Github page
Read the paper
Get it through the Python package index (PyPI) or via conda
YANK
An open, extensible platform for GPU-accelerated alchemical binding free energy calculations using the OpenMM toolkit.
Read the documentation at getyank.org
Go to the YANK GitHub page
Get it through conda
ASSAYTOOLS
A tool for Bayesian inference of binding affinities and other biophysical model parameters from absorbance and fluorescence assays.
Read the documentation at readthedocs
Go to the Github page
Get it via conda
ENSEMBLER
A pipeline for automating omics-scale protein modeling and simulation setup.
Read the documentation at readthedocs
Go to the Github page
Read the paper
Get it via conda
Download the tyrosine kinase models via Dryad
OPEN PATH SAMPLING
A flexible and extensible Python framework for transition interface and path sampling calculations.
Read the documentation at
Go to the Github page
Get it via conda
THERMOPYL
Python tools for retrieving experimental physical property data from the NIST ThermoML Archive.
Read the documentation at readthedocs
Go to the Github page
Read the paper where we use it to automate forcefield benchmarking
Get it via conda
Find more open source tools from our lab on GitHub.