rcsb/rcsb-mcp

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MCP server for RCSB PDB APIs

개요

An MCP server for — discover, inspect, and cross-reference — from LLM clients (Claude Desktop, MCP Inspector, Cursor, etc.). It spans three RCSB APIs: - — find structures with the Search API (keyword, attribute, sequence, chemistry, 3D shape, motif). - — fetch entry / entity / assembly / ligand details and annotations from the Data API. - — map sequences and positional features across PDB, UniProt, and NCBI with the Sequence Coordinates API. Searching is : build a query with an rcsb_query_* tool, then execute it with rcsb_search_request. The builders are pure — they return a query document (readable JSON plus a digest) and touch no network, so . rcsb_query_composer joins two or more documents with AND/OR, which is also how a single search mixes services (e.g. sequence similarity AND an organism filter). Both attribute catalogs are generated from the live metadata schemas by scripts/generate_search_attributes.py.

README

원문 README의 일부입니다. 원문 보기.

rcsb-mcp

An MCP server for interrogating Protein Data Bank structures — discover, inspect, and cross-reference — from LLM clients (Claude Desktop, MCP Inspector, Cursor, etc.). It spans three RCSB APIs:

Discover — find structures with the Search API (keyword, attribute, sequence, chemistry, 3D shape, motif).
Inspect — fetch entry / entity / assembly / ligand details and annotations from the Data API.
Relate — map sequences and positional features across PDB, UniProt, and NCBI with the Sequence Coordinates API.

Tools

Search (search.rcsb.org)

Searching is two steps: build a query with an rcsb_query_* tool, then execute it with rcsb_search_request. The builders are pure — they return a query document (readable JSON plus a digest) and touch no network, so nothing is searched until you call rcsb_search_request. rcsb_query_composer joins two or more documents with AND/OR, which is also how a single search mixes services (e.g. sequence similarity AND an organism filter).

Build

Tool	What it does
`rcsb_query_fulltext`	Free-text keyword query (e.g. `"CRISPR Cas9"`).
`rcsb_query_attribute`	Structured query on one or more indexed attributes (resolution, organism, release date, …) joined by a single `logical_operator`. Each condition supports `exists`, `negation`, `case_sensitive`; `chemical_attributes=True` selects the chemical-component catalog.
`rcsb_query_sequence`	MMseqs2 sequence-similarity query (BLAST-like), with identity / e-value cutoffs.
`rcsb_query_chemical`	Chemical query by SMILES/InChI descriptor (whole-molecule or substructure) or molecular formula.
`rcsb_query_structure`	3D shape-similarity query against a reference PDB assembly or chain.
`rcsb_query_seqmotif`	Short sequence-motif query (PROSITE pattern, regex, or simple wildcards).
`rcsb_query_strucmotif`	3D structural-motif query: a geometric arrangement of specific residues (e.g. a catalytic triad).
`rcsb_query_composer`	Join 2+ query documents with AND/OR — nested boolean logic, and the only way to combine different services in one search.

Run

Tool	What it does
`rcsb_search_request`	Execute a query document and return matching identifiers only. Carries every output option: `return_type`, `limit`/`offset`, `all_hits`, `facets`, `sort_by`/`sort_direction`, `group_by`/`group_by_ranking`, `include_computed_models`.

Discover

Tool	What it does

GitHub에서 전체 README 보기

설치

npx -y mcp-remote https://mcp-beta.rcsb.org/mcp

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설정

{
  "mcpServers": {
    "rcsb-mcp": {
      "type": "http",
      "url": "https://mcp-beta.rcsb.org/mcp"
    }
  }
}