method-physics

The Open Free Energy toolkit

AutoDock Vina

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

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.

Source code for molecular graphics program UCSF ChimeraX

Detect and characterize binding pockets from molecular simulations.

An automated framework for generating optimized partial charges for molecules

A pocket volume analyzer for use in protein modeling.

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.

Reduce - tool for adding and correcting hydrogens in PDB files

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

Solvation Structure and Thermodynamic Mapping

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

Molsystem provides a general class for handling molecular and periodic systems

Force fields produced by the Open Force Field Initiative

A Molecular Topography MultiToolkit designed to simplify and streamline the detection, analysis, and characterization of protein pockets, cavities, channels, and binding sites.

Differentiable, Hardware Accelerated, Molecular Dynamics

A deep learning package for many-body potential energy representation and molecular dynamics

Development version of plumed 2