Cheminformatics

PubChem PUG REST is an HTTP API for retrieving selected chemical records, properties and assay information, with documented identifier inputs, structure searches and operation-specific output formats.

Cheminformatics · Scientific Data

An instruction Skill for using rdkit-agent in cheminformatics workflows, emphasizing chemical-string validation, structured JSON exchange, bounded outputs and documented RDKit WASM limitations.

Cheminformatics

A K-Dense Scientific Agent Skill that guides Datamol-based molecular preparation, similarity analysis, scaffold workflows and conformer handling, with input-validation and reproducibility guidance.

Cheminformatics · Drug Discovery

RDKit Skill (K-Dense) provides procedural guidance, reference material, and Python helpers for molecular parsing, descriptors, similarity screening, substructure filtering, and structure manipulation.

Cheminformatics

ChemCP is an MCP App that turns SMILES strings into interactive 2D molecular diagrams and computed descriptors using RDKit.js, with an in-chat viewer for hosts that support MCP Apps.

Cheminformatics

RDKit MCP Server (TandemAI) connects MCP-capable language models to RDKit tools, with an OpenAI-powered CLI client and an evaluation suite for tool outputs and agent responses.

Cheminformatics

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

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

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

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

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

RxnMapper uses attention from an unsupervised ALBERT model to assign atom mappings to valid reaction SMILES, returning mapped reactions and confidence scores through a Python interface.

Cheminformatics · Reaction Prediction

RDKit is an open-source cheminformatics toolkit for 2D and 3D molecular operations, descriptor and fingerprint generation, and chemical searching through a PostgreSQL cartridge.

Cheminformatics