Open source Java-based chemistry library

A toy molecular dynamics simulator and visualizer

Python-centric Cookiecutter for Molecular Computational Chemistry Packages

A cross-platform command-line utility that creates projects from cookiecutters (project templates), e.g. Python package projects, C projects.

A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution

Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calculations of biomolecules. It works by adding a harmonic boost p…

scripts and facilities for in-silico mutagenesis with FoldX

A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories.

Workshop teaching QMMM using Amber

OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method

Interaction Fingerprints for protein-ligand complexes and more

Rifdock Library for Conformational Search

Jupyter widget to interactively view molecular structures and trajectories

CHARMM and AMBER forcefields for OpenMM (with small molecule support)

Modeling the effects of mutations in proteins using PyRosetta

PDBFixer fixes problems in PDB files

Set of useful HADDOCK utility scripts

A deep learning framework for molecular docking

WebGL protein viewer

Small Code snippets for everyday or borderline problems