DeepMedChem

What you can ask

• Find 20 molecules similar to aspirin, SMILES CC(=O)Oc1ccccc1C(=O)O, in Enamine REAL.
• Search Enamine REAL for shape-similar analogues of c1ccc(CCNc2ncnc3ccccc23)cc1.Copy

  Example path render_results · Chemical space search skill

• Which chemical space databases can I search?

MCP connector

Server URL

https://mcp.deepmedchem.com/mcpCopy

Login

None

Protocol

MCP 2025-11-25

Instructions

Call catalog before similarity_search to obtain current database IDs, methods and guest limits. Run searches sequentially; guest capacity is shared. Searches can create saved CHEESE jobs containing the query and results. Use render_results with the returned result_id to show an earlier grid without another search. Preserve returned CHEESE links exactly. Use verified SMILES; explain unsupported constraints before searching. Scores describe similarity, not biological activity or safety.

Tools

Skills

1 in the ChatGPT listing

• Chemical space searchSearch public DeepMedChem chemical spaces for molecules similar to a supplied structure, and explain the scope of the results.