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

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

Molecule Validation and Standardization

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

• Updated Apr 16, 2020
• Python

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

entity-graph status-active lang-python interface-cli method-deep-learning role-framework domain-cheminformatics method-chemoinformatics entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda domain-drug-discovery method-machine-learning scope-swissknife task-featurization task-molecular-generation domain-computational-chemistry task-property-prediction

• Updated Jul 20, 2026
• Python

Library for reading and writing chemistry files

status-active role-library lang-python lang-cpp domain-cheminformatics task-file-io method-chemoinformatics entity-protein entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused domain-molecular-simulation entity-trajectory

• Updated Jun 19, 2026
• C++

Automated tools for the generation of bespoke SMIRNOFF format parameters for individual 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 task-forcefield ecosystem-openff

• Updated Jul 6, 2026
• Python

Avogadro libraries provide 3D rendering, visualization, analysis and data processing useful in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.

status-active lang-python lang-cpp task-visualization domain-cheminformatics task-file-io task-structure-analysis method-chemoinformatics entity-small-molecule interface-api status-published status-packaged-pypi role-toolkit scope-swissknife entity-crystal domain-computational-chemistry method-quantum

• Updated Jul 30, 2026
• C++

Parameter/topology editor and molecular simulator

status-active role-library lang-python interface-cli domain-cheminformatics task-file-io method-chemoinformatics entity-protein entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused method-physics domain-molecular-simulation task-parameterization task-forcefield

• Updated Jul 1, 2026
• Python

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

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

Web-based molecule sketcher

status-active lang-typescript lang-javascript interface-web task-visualization domain-cheminformatics task-file-io method-chemoinformatics entity-small-molecule status-published scope-focused role-viewer status-packaged-npm

• Updated Jul 29, 2026
• TypeScript

A Pharmacophore MultiToolkit designed to simplify and streamline the detection, generation, analysis, comparison, and application of pharmacophore models in drug-design strategies.

status-active lang-python domain-cheminformatics method-chemoinformatics entity-protein entity-small-molecule interface-api status-published domain-drug-discovery entity-complex role-toolkit scope-suite task-pharmacophore ecosystem-molsys

• Updated May 26, 2026
• Jupyter Notebook

Knowledge-Guided Diffusion Model for 3D Ligand-Pharmacophore Mapping

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 method-diffusion

• Updated Jun 5, 2026
• Python

This repository contains code for the paper: Beyond Generative Models: Superfast Traversal, Optimization, Novelty, Exploration and Discovery (STONED) Algorithm for Molecules using SELFIES

entity-graph role-library lang-python status-archived domain-cheminformatics method-chemoinformatics entity-small-molecule interface-api interface-jupyter status-published scope-focused domain-drug-discovery task-featurization task-molecular-generation

• Updated Aug 13, 2024
• Jupyter Notebook

A package to identify matched molecular pairs and use them to predict property changes.

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

• Updated Jun 3, 2026
• Python

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

Adds or removes hydrogen atoms to achieve the appropriate molecular protonation state for a user-specified pH range

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 domain-drug-discovery method-rule-based task-ligand-prep ecosystem-rdkit

• Updated Dec 13, 2025
• Python

WebGL accelerated JavaScript molecular graphics library

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

• Updated May 22, 2026
• Jupyter Notebook