method-physics

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

The Open Free Energy toolkit

Force fields produced by the Open Force Field Initiative

Detect and characterize binding pockets from molecular simulations.

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

Source code for molecular graphics program UCSF ChimeraX

Solvation Structure and Thermodynamic Mapping

Molsystem provides a general class for handling molecular and periodic systems

Reduce - tool for adding and correcting hydrogens in PDB files

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

A pocket volume analyzer for use in protein modeling.

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.

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.

AutoDock Vina

An automated framework for generating optimized partial charges for molecules

Identification of Protein-Ligand Binding Sites using dipolar EPR data

Powerful, efficient particle trajectory analysis in scientific Python.

MD pharmacophores and virtual screening

Adding hydrogens to molecular models