method-physics

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

The Open Free Energy toolkit

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

AutoDock Vina

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.

Molsystem provides a general class for handling molecular and periodic systems

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.

Detect and characterize binding pockets from molecular simulations.

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

Reduce - tool for adding and correcting hydrogens in PDB files

Solvation Structure and Thermodynamic Mapping

Source code for molecular graphics program UCSF ChimeraX

Force fields produced by the Open Force Field Initiative

An automated framework for generating optimized partial charges for molecules

Adding hydrogens to molecular models

Experiments with expanded ensembles to explore chemical space

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

Development version of plumed 2