MCP Servers

ChemGraph is a Python agent framework that connects natural-language chemistry requests to molecular construction, simulations, analysis, and reporting, with CLI, Python, Streamlit, and MCP interfaces.

Computational Chemistry · Materials Discovery

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

NovoMCP exposes computational chemistry tools through MCP and REST, combining molecular profiling with configurable simulation services, discovery-funnel orchestration, and tool-call auditing.

Computational Chemistry · Drug Discovery

PocketScout MCP equips AI assistants to assess known protein binding sites using public structural, bioactivity, conservation, variant, and literature data before target selection or binder design.

Drug Discovery · Scientific Data

Benchling MCP (longevity-genie) is a Python MCP server that connects AI clients to Benchling notebook entries, biological sequences, projects, and entity search using API credentials.

Lab Automation · Scientific Data

PubMed MCP (cyanheads) is a third-party MCP server connecting AI clients to biomedical literature search, article metadata, available full text, MeSH vocabulary and citation tools.

Literature & Research · Drug Discovery

A third-party MCP server that connects assistant clients to Materials Project through mp_api, with tools for material searches, crystal structures, electronic properties, and other materials data.

Materials Discovery · Scientific Data

RCSB MCP (cnyambura) is a third-party MCP server that exposes RCSB PDB entry and polymer metadata, structure downloads, and custom Data API queries to an MCP client.

Drug Discovery · Scientific Data

UniProt MCP (cyanheads) is a third-party MCP server that connects AI clients to UniProt protein search, annotations, identifier mapping, proteomes, taxonomy, and amino-acid sequences.

Drug Discovery · Scientific Data

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

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