Reduce - tool for adding and correcting hydrogens in PDB files
The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io
An automated framework for generating optimized partial charges for molecules
A pocket volume analyzer for use in protein modeling.
The Open Free Energy toolkit
Source code for molecular graphics program UCSF ChimeraX
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.
Solvation Structure and Thermodynamic Mapping
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.
OpenMM is a toolkit for molecular simulation using high performance GPU code.
Force fields produced by the Open Force Field Initiative
Molsystem provides a general class for handling molecular and periodic systems
End-To-End Molecular Dynamics (MD) Engine using PyTorch
Powerful, efficient particle trajectory analysis in scientific Python.
Identification of Protein-Ligand Binding Sites using dipolar EPR data
Adding hydrogens to molecular models
Experiments with expanded ensembles to explore chemical space
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