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

status-active lang-python lang-cpp role-framework entity-protein entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused method-physics domain-molecular-simulation entity-trajectory interface-gpu lang-cuda ecosystem-openmm task-md-engine

• Updated Jul 27, 2026
• C++

Detect and characterize binding pockets from molecular simulations.

status-active lang-python interface-cli role-application entity-protein interface-api status-published scope-focused domain-drug-discovery task-pocket-detection method-physics method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory

• Updated Mar 17, 2026
• Python

Source code for molecular graphics program UCSF ChimeraX

status-active lang-python lang-cpp task-visualization interface-cli domain-structural-biology task-file-io task-structure-analysis method-chemoinformatics entity-protein entity-small-molecule interface-api status-published method-physics entity-complex scope-swissknife entity-nucleic-acid interface-gui role-viewer

• Updated Jul 29, 2026
• Python

An automated framework for generating optimized partial charges for molecules

status-active role-library lang-python interface-cli domain-cheminformatics method-chemoinformatics entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused method-physics domain-molecular-simulation task-parameterization ecosystem-openff task-charge-assignment

• Updated Jul 6, 2026
• Python

The Open Free Energy toolkit

status-active lang-python interface-cli role-framework entity-protein entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda domain-drug-discovery method-physics entity-complex method-statistics domain-molecular-simulation scope-suite ecosystem-openmm task-free-energy ecosystem-openfe

• Updated Jul 29, 2026
• Python

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

status-active lang-python domain-cheminformatics method-chemoinformatics entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda method-physics domain-molecular-simulation role-toolkit scope-suite task-parameterization ecosystem-rdkit task-forcefield ecosystem-openff

• Updated Jul 27, 2026
• Python

Force fields produced by the Open Force Field Initiative

status-active lang-python entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda method-physics domain-molecular-simulation scope-suite task-forcefield ecosystem-openff role-dataset

• Updated Jul 6, 2026
• Python

status-archived lang-c interface-cli role-application domain-structural-biology entity-protein entity-small-molecule status-published scope-focused domain-drug-discovery task-docking method-physics ecosystem-autodock task-featurization

• Updated Dec 7, 2024
• C++

Molsystem provides a general class for handling molecular and periodic systems

status-active role-library lang-python domain-cheminformatics method-chemoinformatics entity-protein entity-small-molecule interface-api status-published status-packaged-pypi scope-focused method-physics domain-molecular-simulation task-system-model entity-crystal

• Updated Jun 30, 2026
• Python

Solvation Structure and Thermodynamic Mapping

status-active lang-python lang-cpp interface-cli role-application entity-protein interface-api status-published scope-focused domain-drug-discovery method-physics method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory task-free-energy

• Updated Dec 17, 2025
• Python

Reduce - tool for adding and correcting hydrogens in PDB files

status-active lang-cpp interface-cli role-application domain-structural-biology entity-protein status-published status-packaged-conda scope-focused method-physics entity-nucleic-acid task-structure-prep method-rule-based

• Updated Jan 5, 2026
• C++

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.

status-active lang-c interface-cli role-application domain-structural-biology entity-protein status-published status-packaged-conda scope-focused domain-drug-discovery task-pocket-detection task-binding-site method-physics

• Updated Mar 9, 2026
• C

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.

lang-python status-archived task-visualization role-application domain-structural-biology method-chemoinformatics entity-protein entity-small-molecule interface-jupyter status-published scope-focused domain-drug-discovery task-docking method-physics entity-complex

• Updated Oct 30, 2023
• Jupyter Notebook

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

status-active lang-python method-deep-learning role-framework entity-small-molecule interface-api status-published status-packaged-pypi scope-focused method-physics domain-molecular-simulation entity-trajectory interface-gpu task-md-engine task-ml-potential

• Updated Apr 21, 2026
• Python

A pocket volume analyzer for use in protein modeling.

lang-python status-archived interface-cli role-application domain-structural-biology entity-protein interface-api status-published status-packaged-pypi scope-focused domain-drug-discovery task-pocket-detection method-physics method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory

• Updated Oct 2, 2022
• Python

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

status-active lang-python lang-cpp method-deep-learning role-framework entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused method-physics domain-molecular-simulation entity-trajectory interface-gpu lang-cuda entity-crystal task-md-engine domain-computational-chemistry task-ml-potential

• Updated Jul 29, 2026
• Python

Development version of plumed 2

status-active lang-python lang-cpp interface-cli role-plugin entity-protein entity-small-molecule interface-api status-published status-packaged-conda scope-focused method-physics method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory task-free-energy

• Updated Jul 20, 2026
• C++

pythonic interface to virtual screening software

status-active role-library lang-python interface-cli task-workflow role-application domain-cheminformatics method-chemoinformatics entity-protein entity-small-molecule interface-api status-published status-packaged-pypi scope-focused domain-drug-discovery task-docking method-physics entity-complex

• Updated Sep 4, 2025
• Python

Public development project of the LAMMPS MD software package

status-active lang-python lang-cpp interface-cli role-framework entity-small-molecule interface-api status-published status-packaged-conda scope-focused method-physics domain-molecular-simulation entity-trajectory interface-gpu lang-cuda entity-crystal task-md-engine domain-materials

• Updated Jul 28, 2026
• C++

MD pharmacophores and virtual screening

lang-python status-archived interface-cli role-application method-chemoinformatics entity-protein entity-small-molecule interface-api status-published status-packaged-pypi scope-focused domain-drug-discovery method-physics entity-complex domain-molecular-simulation task-trajectory-analysis entity-trajectory task-pharmacophore

• Updated Dec 15, 2023
• Python