method-physics

Molsystem provides a general class for handling molecular and periodic systems

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.

Force fields produced by the Open Force Field Initiative

The Open Free Energy toolkit

AutoDock Vina

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

Detect and characterize binding pockets from molecular simulations.

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.

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

A pocket volume analyzer for use in protein modeling.

Reduce - tool for adding and correcting hydrogens in PDB files

An automated framework for generating optimized partial charges for molecules

Public development project of the LAMMPS MD software package

pythonic interface to virtual screening software

Adding hydrogens to molecular models

Experiments with expanded ensembles to explore chemical space