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deep-medchem/deepmedchem

v0.1.0MIT

Search public chemical spaces by molecular similarity with DeepMedChem.

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DeepMedChem plugin for Claude

Search public DeepMedChem chemical spaces for molecules similar to a structure you supply, directly from Claude.

The plugin contains no server code or credentials. It connects Claude to the remote MCP service at https://mcp.deepmedchem.com/mcp, which DeepMedChem operates, and adds a skill that tells Claude how to use it.

What it does

  • catalog: lists the available databases, their pricing and the guest limits.
  • similarity_search: searches one SMILES against one database for up to 20 hits, using morgan (fingerprint), shape or esp (electrostatic) similarity.
  • render_results: shows an earlier result again by its result_id.

In hosts that support MCP Apps, results appear as an interactive structure grid with CSV export and a link to the vendor's catalogue. The response also includes a CHEESE link that runs the same search again in the web app; it does not reopen the exact stored shortlist.

Guest access needs no signup, and all guests share the same capacity, so run one search at a time. A "busy" error means the shared capacity is in use; wait a moment and try again. For larger searches, substructure queries or persistent work, use a DeepMedChem account with the Python SDK.

Install

/plugin marketplace add Deep-MedChem/deepmedchem-claude-plugin
/plugin install deepmedchem

Whether Claude can reach the remote server depends on your Claude workspace's connector policy.

ChatGPT

The same plugin is packaged for ChatGPT: plugin.json, mcp.json, skills/ and assets/ at the repository root. Download the ZIP from the latest release, or build it with scripts/build-openai-zip.sh. Submission details are in OPENAI_SUBMISSION.md.

Limits

Similarity scores measure structural similarity. They are not predictions of biological activity or safety. Vendors determine availability and synthesis. Prices are list prices in USD for the default 1 mg amount shipped to the US, as reported by the catalogue; many make-on-demand products share the same price tier. Results are a bounded shortlist, not every match.

Data and privacy

The plugin runs no code on your machine and installs nothing. It only declares the remote MCP server and a skill.

  • What is sent: the SMILES you search, the chosen database, method and result count, plus a result_id when an earlier result is shown again. Nothing else from the conversation is sent.
  • Where it goes: https://mcp.deepmedchem.com, operated by Deep MedChem, which forwards the search to the DeepMedChem API. No third party receives the query.
  • No account or credentials are used, and the plugin never asks for an API key.
  • Results are kept in server memory so that render_results and the CSV export can return them. They are discarded when newer results replace them or the server restarts, so there is no fixed retention period, and old result links can stop working.
  • Links in the results grid open the vendor's general catalogue page (and the CHEESE link opens https://cheese.deepmedchem.com) in your browser only when you click them.

Privacy policy: https://cheese.deepmedchem.com/privacy-policy. Terms: https://cheese.deepmedchem.com/terms-and-conditions.

Support

Email info@deepmedchem.com, or open an issue in this repository.

License

MIT