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Pymatgen is a Python materials-analysis library combining structure and file-format support with phase diagrams, electronic-structure analysis, thermodynamic calculations and database integrations.

Materials Discovery

Chemistry Development Kit (CDK) is a Java library for chemical representations, file conversion, structure searching, fingerprints, QSAR descriptors and molecular rendering within other programs.

Cheminformatics

Open Babel is a chemical data toolkit with ready-to-use programs and a Python interface for format conversion, molecular searching, and 2D or 3D coordinate generation.

Cheminformatics

Mordred is a Python molecular descriptor calculator with command-line and RDKit-based library workflows, producing descriptor tables for cheminformatics analysis and downstream model evaluation.

Molecular Property Prediction · Cheminformatics

SELFIES is a molecular string representation and Python library for translating SMILES, preparing token encodings, and generating molecular graphs under configurable semantic constraints.

Molecular Generation · Cheminformatics

Datamol is a Python molecular-processing library built on RDKit, with tools for structure conversion, standardization, fingerprints, conformers, visualization and local or remote file I/O.

Cheminformatics

Molfeat is a Python toolkit for small-molecule featurization, combining molecular fingerprints, descriptors and pretrained embeddings with parallel transformation, caching and extensible plugins.

Molecular Property Prediction · Cheminformatics

DeepPurpose is a PyTorch-based toolkit for training and applying compound and protein prediction models, with workflows for drug-target interactions, molecular properties, repurposing and virtual screening.

Drug Discovery

TorchDrug is a PyTorch-based toolkit for graph and molecular machine learning, with SMILES input, graph operations, property-prediction building blocks and multi-CPU/GPU execution.

Molecular Property Prediction · Drug Discovery

PubChemPy is a Python wrapper for the PubChem PUG REST API, supporting chemical searches, compound-property retrieval, standardization, file-format conversion and depiction.

Cheminformatics · Scientific Data

QCArchive supports running, storing and sharing quantum chemistry calculations through a database-backed server, a Python client and computation workers maintained in one repository.

Quantum Chemistry · Scientific Data

Official Python client maintained by the ChEMBL group for querying ChEMBL data and cheminformatics services, with QuerySet-style filters, lazy retrieval and local result caching.

Drug Discovery · Scientific Data

Materials Project API is the Python client project published as mp-api, with official data-access documentation and an optional MCP server entry point declared in its package configuration.

Materials Discovery · Scientific Data

PubChem MCP (PhelanShao) is a Python MCP server that lets AI clients retrieve PubChem compound properties and structures by name or CID, with JSON, CSV, XYZ and downloadable structure-file outputs.

Cheminformatics · Scientific Data

ChEMBL MCP (cyanheads) connects MCP clients to ChEMBL compound, target, bioactivity and drug records, with structure searches and optional DuckDB analysis of larger activity sets.

Drug Discovery · Scientific Data

PubChem MCP (cyanheads) connects MCP clients to PubChem compound and bioassay data, with identifier and structure searches, property retrieval, safety records, cross-references and 3D conformers.

Cheminformatics · Scientific Data

Scientific Agent Skills provides procedural guidance for AI agents working with scientific packages, databases and research workflows, including cheminformatics, spectroscopy and materials analysis.

Cheminformatics · Scientific Data

Coscientist provides a simple implementation and supporting research data for large-language-model chemical research, covering synthesis planning, library selections, repeated runs and optimization.

Literature & Research · Lab Automation

PaperQA provides agentic retrieval-augmented question answering over scientific documents, combining local search, ranked evidence summaries and answers with in-text citations.

Literature & Research

ChemCrow is a Python chemistry agent package built with Langchain that connects language-model reasoning to RDKit, paper-qa, chemical databases, and reaction-planning tools.

Cheminformatics · Literature & Research