Cryptic binding pocket discovery from conformational ensembles. Open-source, reproducible, size-robust benchmarks against fpocket, PocketMiner and CryptoBench.

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

• Updated Jul 23, 2026
• Python

PyRod - Tracing water molecules in molecular dynamics simulations

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

• Updated Oct 31, 2025
• Python

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

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++

Toolbox for molecular animations in Blender, powered by Geometry Nodes.

status-active lang-python task-visualization role-plugin domain-structural-biology method-chemoinformatics entity-protein entity-small-molecule scope-focused domain-molecular-simulation entity-trajectory interface-gui role-viewer

• Updated Jul 29, 2026
• Python

🏗️ Statistical models for biomolecular dynamics 🏗️

lang-python status-archived entity-protein interface-api status-published status-packaged-conda scope-focused method-machine-learning method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory role-toolkit

• Updated Jan 26, 2021
• Python

WebGL protein viewer

status-active lang-typescript lang-javascript interface-web task-visualization domain-structural-biology method-chemoinformatics entity-protein entity-small-molecule interface-api status-published scope-focused entity-trajectory role-viewer status-packaged-npm

• Updated Apr 14, 2025
• TypeScript

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

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++

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

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

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

Differentiable, Hardware Accelerated, Molecular Dynamics

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 entity-crystal task-md-engine task-ml-potential

• Updated Jul 26, 2026
• Jupyter Notebook

🚂 Python API for Emma's Markov Model Algorithms 🚂

lang-python status-archived entity-protein interface-api status-published status-packaged-pypi status-packaged-conda scope-focused method-machine-learning method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory role-toolkit

• Updated Sep 11, 2023
• Python

A comprehensive macromolecular library

status-active lang-typescript lang-javascript interface-web task-visualization domain-structural-biology method-chemoinformatics entity-protein entity-small-molecule interface-api status-published scope-focused entity-complex entity-trajectory role-viewer status-packaged-npm

• Updated Jul 29, 2026
• TypeScript

Powerful, efficient particle trajectory analysis in scientific Python.

status-active role-library lang-python lang-cpp task-structure-analysis interface-api status-published status-packaged-pypi status-packaged-conda scope-focused method-physics method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory entity-crystal domain-materials

• Updated Jul 29, 2026
• C++

Library for computing dynamic non-covalent contact networks in proteins throughout MD Simulation

status-active lang-python interface-cli role-application domain-structural-biology entity-protein status-published scope-focused entity-complex domain-molecular-simulation task-trajectory-analysis entity-trajectory method-rule-based task-interaction-analysis

• Updated Jun 28, 2026
• Python

Fast and All atom Protein-Ligand Interaction Profiler

status-active role-library lang-python interface-cli domain-structural-biology entity-protein entity-small-molecule interface-api status-packaged-pypi scope-focused domain-drug-discovery entity-complex task-trajectory-analysis entity-trajectory method-rule-based interface-gpu task-interaction-analysis

• Updated Jul 27, 2026
• Python

Dynamic pharmacophore modeling of molecular interactions

role-library lang-python status-archived method-chemoinformatics entity-protein entity-small-molecule interface-api interface-jupyter status-published status-packaged-conda domain-drug-discovery entity-complex method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory scope-swissknife task-pharmacophore task-interaction-analysis

• Updated Apr 26, 2024
• Promela

An open library for the analysis of molecular dynamics trajectories

status-active lang-python lang-c task-file-io task-structure-analysis entity-protein entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda method-physics method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory role-toolkit scope-swissknife

• Updated Jul 29, 2026
• Python