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
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 Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io
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.
End-To-End Molecular Dynamics (MD) Engine using PyTorch
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.
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
A Molecular Topography MultiToolkit designed to simplify and streamline the detection, analysis, and characterization of protein pockets, cavities, channels, and binding sites.
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