method-physics

A pocket volume analyzer for use in protein modeling.

Solvation Structure and Thermodynamic Mapping

Source code for molecular graphics program UCSF ChimeraX

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

Reduce - tool for adding and correcting hydrogens in PDB files

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

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.

Detect and characterize binding pockets from molecular simulations.

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.

An automated framework for generating optimized partial charges for molecules

AutoDock Vina

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

Molsystem provides a general class for handling molecular and periodic systems

The Open Free Energy toolkit

Force fields produced by the Open Force Field Initiative

A Molecular Topography MultiToolkit designed to simplify and streamline the detection, analysis, and characterization of protein pockets, cavities, channels, and binding sites.

Differentiable, Hardware Accelerated, Molecular Dynamics

Adding hydrogens to molecular models

Experiments with expanded ensembles to explore chemical space