Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.

End-To-End Molecular Dynamics (MD) Engine using PyTorch

The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io

The Open Free Energy toolkit

AutoDock Vina

OpenMM plugin to define forces with neural networks

An automated framework for generating optimized partial charges for molecules

Molsystem provides a general class for handling molecular and periodic systems

fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level. fpocket is distributed as free open source software.

Force fields produced by the Open Force Field Initiative

OpenMM is a toolkit for molecular simulation using high performance GPU code.

pythonic interface to virtual screening software

Public development project of the LAMMPS MD software package

A project (and object) for storing, manipulating, and converting molecular mechanics data.

A deep learning framework for molecular docking

Identification of Protein-Ligand Binding Sites using dipolar EPR data

Powerful, efficient particle trajectory analysis in scientific Python.

Parameter/topology editor and molecular simulator

A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.