MCP servers that ship as code — a repository or a package you install and run locally (usually over stdio). They have no hosted endpoint, so we cannot probe or grade them: instead each one shows its repository, install command, license, stars and when it was last updated.
Collected from GitHub repositories and npm, PyPI, Cargo, Go, Maven, NuGet and RubyGems packages tagged as MCP servers, the official MCP Registry, Docker's MCP catalog, ModelScope, Baidu MCP World, Cline and other public directories; one entry per repository. A server that also offers a hosted endpoint is listed under Remote instead. These entries are not counted in our reachability, verification or readiness statistics.
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rdkit-mcp-servergithub.com/tandemai-inc/rdkit-mcp-serverupdated this year
MCP server that enables language models to interact with RDKit through natural language
MIT ★ 48 -
MCP server that draws structures, reactions, mechanisms, peptides and proteins for Claude. Structures are drawn locally with RDKit; names, data sheets and proteins are looked up online.
pypi Apache-2.0 ★ 32 -
Search PubChem by chemical structure: a local similarity and substructure index, live PubChem tools, a CLI and an MCP server
pypi MIT -
smiles2iupacgithub.com/gvmfhy/smiles2iupacupdated this year
Free, open-source SMILES → IUPAC name converter. PubChem-keyed lookup with OPSIN round-trip cross-validation. CLI, Python lib, Gradio web app, MCP server.
MIT ★ 2 -
Machine-learning oral drug-likeness score for small molecules (SMILES in, 0–1 out), with an MCP server for AI assistants (Claude, Cursor, VS Code and other MCP clients). J. Chem. Inf. Model. 2026.
MIT ★ 4