method-physics

AutoDock Vina

An automated framework for generating optimized partial charges for molecules

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.

Molsystem provides a general class for handling molecular and periodic systems

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

Source code for molecular graphics program UCSF ChimeraX

Reduce - tool for adding and correcting hydrogens in PDB files

Force fields produced by the Open Force Field Initiative

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

Solvation Structure and Thermodynamic Mapping

The Open Free Energy toolkit

Detect and characterize binding pockets from molecular simulations.

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.

A pocket volume analyzer for use in protein modeling.

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

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

Development version of plumed 2

Experiments with expanded ensembles to explore chemical space

Adding hydrogens to molecular models