Click on "Deploy Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type @ followed by the MCP server name and your instructions, e.g., "@mcp-bindingdb What's the binding affinity of imatinib for ABL1?"
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
Under construction: this project is in early development. Tools, table layouts and examples may change without notice.
An MCP server that lets Claude query BindingDB: about 3.2M measured protein–ligand binding affinities for 1.5M compounds and 13k targets, from a local, read-only copy.
Seventeen worked examples show real questions answered with these tools, such as the most potent EGFR ligands, imatinib's selectivity profile, analogues of palbociclib, the targets of a chemotype, and turning a chemical name into a structure. Each shows the tool calls, the results and the answer.
Related MCP server: guidetopharmacology
Install uv and Docker (needed only to build the database), and optionally a Java runtime (for IUPAC-name parsing). Then clone the repository:
git clone https://github.com/pwrose/mcp-bindingdb.git
cd mcp-bindingdbBuild the database (downloads the BindingDB dump; needs about 5 GB of disk space):
scripts/build_duckdb.shSee Building the database for releases and options.
Add the server to Claude.
Claude Desktop: add this to claude_desktop_config.json (Settings → Developer → Edit Config) and
restart Claude:
{
"mcpServers": {
"mcp-bindingdb": {
"command": "uv",
"args": ["--directory", "/path/to/mcp-bindingdb", "run", "--extra", "substructure", "--extra", "name",
"mcp-bindingdb"]
}
}
}Claude Code: the repository's .mcp.json registers the server when you run claude in this
folder. To use it from any folder:
claude mcp add --scope user mcp-bindingdb -- uv --directory /path/to/mcp-bindingdb run --extra substructure --extra name mcp-bindingdbIf some tools are missing in a chat, check that they are switched on in the chat's tools menu.
Tool | Purpose |
| Find compounds by name/synonym, ChEMBL id, |
| SMILES for a compound name (trade name, IUPAC name, CAS number), with the BindingDB compounds that have that structure |
| Find targets by name, gene name, UniProt entry name or accession |
| Identifiers, synonyms, PDB ligands, most potent targets |
| Identifiers, synonyms, PDB ids, complex components, measurement counts |
| Most potent compounds for a target |
| Activity/selectivity profile of a compound |
| Full record of one measurement, with assay description and citation |
| Compounds containing a SMILES/SMARTS fragment, or the targets they were measured against |
| Compounds similar to a molecule, or the targets they were measured against |
| Table list with descriptions, or the columns of one table |
| Any read-only SQL query |
All tools are read-only. Only chemical_name_to_smiles uses the network, to look names up in PubChem.
See Tools for how the searches work and notes on the data.
Building the database: releases, derived tables, structure-search index
Tools: tool details, safety, data notes
Development: running the server by hand, server options, tests, regenerating examples
BSD 3-Clause; see LICENSE. BindingDB data are subject to BindingDB's own terms.
This server cannot be deployed
BindingDB — measured protein/small-molecule binding affinities.
Link compounds to protein targets, rank bioactivity, and look up drug mechanisms and indications.
Query, join, profile, clean and convert CSV/JSON/Parquet with server-side DuckDB over MCP.
Biomedical data: compounds, drug info, and molecular targets