method-physics

AutoDock Vina

Reduce - tool for adding and correcting hydrogens in PDB files

A pocket volume analyzer for use in protein modeling.

Source code for molecular graphics program UCSF ChimeraX

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

Force fields produced by the Open Force Field Initiative

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.

The Open Free Energy toolkit

Molsystem provides a general class for handling molecular and periodic systems

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

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

An automated framework for generating optimized partial charges for molecules

Adding hydrogens to molecular models

Experiments with expanded ensembles to explore chemical space

MD pharmacophores and virtual screening

Public development project of the LAMMPS MD software package