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

Some useful RDKit functions

status-active role-library lang-python domain-cheminformatics task-file-io method-chemoinformatics entity-small-molecule interface-api status-packaged-pypi scope-focused domain-drug-discovery task-featurization ecosystem-rdkit

• Updated Jun 1, 2026
• 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

Calculation of interatomic interactions in molecular structures

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

• Updated Sep 3, 2024
• Python

A project (and object) for storing, manipulating, and converting molecular mechanics data.

status-active role-library lang-python task-file-io entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda method-physics domain-molecular-simulation scope-suite task-system-model task-forcefield ecosystem-openff ecosystem-openmm

• Updated Jul 27, 2026
• Python

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

status-active lang-python domain-structural-biology method-chemoinformatics entity-protein interface-api status-published domain-drug-discovery task-pocket-detection task-binding-site method-physics role-toolkit scope-suite ecosystem-molsys

• Updated Jul 5, 2026
• Jupyter Notebook

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

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

Official Github for "PharmacoNet: deep learning-guided pharmacophore modeling for ultra-large-scale virtual screening" (Chemical Science)

status-active lang-python interface-cli method-deep-learning role-application domain-cheminformatics entity-protein entity-small-molecule interface-api status-published scope-focused domain-drug-discovery entity-complex interface-gpu task-pharmacophore

• Updated Jul 15, 2025
• Python

Open-Source Quantum Chemistry – an electronic structure package in C++ driven by Python

status-active lang-python lang-cpp interface-cli entity-small-molecule interface-api status-published status-packaged-conda scope-focused role-toolkit domain-computational-chemistry task-quantum-chemistry method-quantum

• Updated Jul 24, 2026
• C++

Reaction fingerprints, atlases and classification. Code complementing our Nature Machine Intelligence publication on "Mapping the space of chemical reactions using attention-based neural networks" (http://rdcu.be/cenmd).

entity-graph role-library lang-python status-archived method-deep-learning domain-cheminformatics method-chemoinformatics entity-small-molecule interface-api status-published status-packaged-pypi scope-focused task-featurization task-retrosynthesis

• Updated Aug 12, 2021
• HTML

Molecular Processing Made Easy.

entity-graph status-active role-library lang-python domain-cheminformatics task-file-io method-chemoinformatics entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused domain-drug-discovery task-featurization ecosystem-rdkit

• Updated May 20, 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

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++

ChEMBL database structure pipelines

status-active role-library lang-python domain-cheminformatics task-file-io method-chemoinformatics entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused domain-drug-discovery method-rule-based task-ligand-prep ecosystem-rdkit

• Updated Nov 24, 2025
• Python

Semiempirical Extended Tight-Binding Program Package

status-active interface-cli role-application entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused entity-crystal task-charge-assignment domain-computational-chemistry task-quantum-chemistry method-quantum lang-fortran

• Updated Jul 13, 2026
• Fortran

macromolecular crystallography library and utilities

status-active lang-python lang-cpp interface-cli domain-structural-biology task-file-io task-structure-analysis method-chemoinformatics entity-protein interface-api status-published status-packaged-pypi status-packaged-conda method-statistics role-toolkit scope-swissknife task-structure-prep entity-crystal domain-crystallography

• Updated Jul 24, 2026
• C++

📐 Symmetry-corrected RMSD in Python

status-active role-library lang-python interface-cli domain-cheminformatics task-structure-analysis method-chemoinformatics entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused domain-drug-discovery entity-complex

• 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

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