method-physics

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

Reduce - tool for adding and correcting hydrogens in PDB files

Solvation Structure and Thermodynamic Mapping

The Open Free Energy toolkit

Source code for molecular graphics program UCSF ChimeraX

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

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.

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.

AutoDock Vina

Detect and characterize binding pockets from molecular simulations.

Force fields produced by the Open Force Field Initiative

Molsystem provides a general class for handling molecular and periodic systems

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

A pocket volume analyzer for use in protein modeling.

An automated framework for generating optimized partial charges for molecules

Powerful, efficient particle trajectory analysis in scientific Python.

Identification of Protein-Ligand Binding Sites using dipolar EPR data

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