Is io.github.rcsb/rcsb-mcp safe to use?

io.github.rcsb/rcsb-mcp has no known CVEs as of the latest MCPpedia security scan. Authentication requirements were not detected automatically - check the project's documentation before connecting in a shared environment. Licensed under MIT.

How do I install io.github.rcsb/rcsb-mcp?

io.github.rcsb/rcsb-mcp supports copy-paste install configs on its MCPpedia page for Claude Desktop, Cursor, and Claude Code. Scroll to the Quick Install section and select your client.

What can io.github.rcsb/rcsb-mcp do?

io.github.rcsb/rcsb-mcp provides 13 tools: sequence, structural, rcsb_search_by_sequence, rcsb_search_by_structure, facets and 8 more. See the full tools list on the server page for descriptions and parameters.

What AI clients work with io.github.rcsb/rcsb-mcp?

io.github.rcsb/rcsb-mcp is compatible with claude-desktop, cursor, claude-code. It uses stdio and sse transport.

Is io.github.rcsb/rcsb-mcp actively maintained?

io.github.rcsb/rcsb-mcp is actively maintained - last commit was 5 days ago. It has 11 GitHub stars.

io.github.rcsb/rcsb-mcp

rcsb-mcp

MCP server to search, inspect, and cross-reference RCSB Protein Data Bank structures

11 13 tools GitHub PyPI

No known CVEs

MIT license

Actively maintained

Last commit 5d ago

Works with most clients

Transport: stdio, sse

13 tools · ~515 tok

Grade B · 0.3% of 200K ctx

MCPpedia last refreshed this data 22h ago

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io.github.rcsb/rcsb-mcp is an MCP server that MCP server to search, inspect, and cross-reference RCSB Protein Data Bank structures. Its tool list has not been published yet over stdio and sse, requires no API key, and scores 82/100 on MCPpedia's security, maintenance and efficiency rubric.

Other

Step 1

Install in your client

Config is the same across clients - only the file and path differ.

Supported in Claude Desktopstdio, sse · Node 18+

Paste into ~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "rcsb-mcp": {
      "args": [
        "rcsb-mcp"
      ],
      "command": "uvx"
    }
  }
}

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[![MCPpedia Score](https://mcppedia.org/api/badge/io-github-rcsb-rcsb-mcp)](https://mcppedia.org/s/io-github-rcsb-rcsb-mcp)

Read me

What io.github.rcsb/rcsb-mcp does

MCP server to search, inspect, and cross-reference RCSB Protein Data Bank structures

Test This Server

This server supports HTTP transport. Be the first to test it - help the community know if it works.

Loading README…

Scored, not listed

Why this score

Five weighted categories - click any category to see the underlying evidence.

Score breakdown

82/100across 5 weighted dimensions

How we score →

0255075100

−18

Security

Maintenance

Efficiency

Documentation

Compatibility

Categoriesclick a row to see evidence

Security

OSV.dev

No known CVEs.

Checked rcsb-mcp against OSV.dev.

Inventory

Tools (13)

Click any tool to inspect its schema.

~515 tokens total

Community

Reviews

Be the first to review

Have you used this server?

Share your experience - it helps other developers decide.

How easy was setup?Did it work reliably?How was the documentation?

Frequently Asked Questions

Is io.github.rcsb/rcsb-mcp safe to use?: io.github.rcsb/rcsb-mcp has no known CVEs as of the latest MCPpedia security scan. Authentication requirements were not detected automatically - check the project's documentation before connecting in a shared environment. Licensed under MIT.
How do I install io.github.rcsb/rcsb-mcp?: io.github.rcsb/rcsb-mcp supports copy-paste install configs on its MCPpedia page for Claude Desktop, Cursor, and Claude Code. Scroll to the Quick Install section and select your client.
What can io.github.rcsb/rcsb-mcp do?: io.github.rcsb/rcsb-mcp provides 13 tools: sequence, structural, rcsb_search_by_sequence, rcsb_search_by_structure, facets and 8 more. See the full tools list on the server page for descriptions and parameters.
What AI clients work with io.github.rcsb/rcsb-mcp?: io.github.rcsb/rcsb-mcp is compatible with claude-desktop, cursor, claude-code. It uses stdio and sse transport.
Is io.github.rcsb/rcsb-mcp actively maintained?: io.github.rcsb/rcsb-mcp is actively maintained - last commit was 5 days ago. It has 11 GitHub stars.

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Community

Discussion

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Other

Step 1

Install in your client

Config is the same across clients - only the file and path differ.

Supported in Claude Desktopstdio, sse · Node 18+

Paste into ~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "rcsb-mcp": {
      "args": [
        "rcsb-mcp"
      ],
      "command": "uvx"
    }
  }
}

Are you the author?

Add this badge to your README to show your security score and help users find safe servers.

Embed in your READMEAbout badges →

[![MCPpedia Score](https://mcppedia.org/api/badge/io-github-rcsb-rcsb-mcp)](https://mcppedia.org/s/io-github-rcsb-rcsb-mcp)

Read me

What io.github.rcsb/rcsb-mcp does

MCP server to search, inspect, and cross-reference RCSB Protein Data Bank structures

Test This Server

This server supports HTTP transport. Be the first to test it - help the community know if it works.

README

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
`rcsb_list_pdb_search_attributes`	Discover searchable attribute paths, types, and operators. `schema="structure"` (default, ~636) or `schema="chemical"` (~58: `chem_comp.`, `drugbank_info.`, ...). Records also carry `enum` (closed value sets) and `nested_group` (attributes stored in nested objects — see below).
`rcsb_find_go_terms`	Resolve a free-text molecular function / biological process / cellular component to Gene Ontology ids (via EBI QuickGO), annotated with PDB entry counts — then search by `rcsb_polymer_entity_annotation.annotation_lineage.id`.
`rcsb_find_interpro_domains`	Resolve a free-text protein domain / family / fold to InterPro and Pfam ids (via EBI Search), annotated with PDB entry counts — then search by `rcsb_polymer_entity_annotation.annotation_id`.
`rcsb_find_enzyme_classes`	Resolve a free-text enzyme / reaction to Enzyme Commission (EC) numbers (via EBI Search/IntEnz), annotated with PDB entry counts — then search by `rcsb_polymer_entity.rcsb_ec_lineage.id` (hierarchical).
`rcsb_find_disease_terms`	Resolve a free-text disease / condition to MONDO ids (via EBI OLS), annotated with PDB entry counts — then search by `rcsb_uniprot_annotation.annotation_lineage.id` (hierarchi

... View full README on GitHub

Loading README…

Scored, not listed

Why this score

Five weighted categories - click any category to see the underlying evidence.

Score breakdown

82/100across 5 weighted dimensions

How we score →

0255075100

−18

Security

Maintenance

Efficiency

Documentation

Compatibility

Categoriesclick a row to see evidence

Security

OSV.dev

No known CVEs.

Checked rcsb-mcp against OSV.dev.

Inventory

Tools (13)

Click any tool to inspect its schema.

~515 tokens total

Community

Reviews

Be the first to review

Have you used this server?

Share your experience - it helps other developers decide.

How easy was setup?Did it work reliably?How was the documentation?

Frequently Asked Questions

Is io.github.rcsb/rcsb-mcp safe to use?: io.github.rcsb/rcsb-mcp has no known CVEs as of the latest MCPpedia security scan. Authentication requirements were not detected automatically - check the project's documentation before connecting in a shared environment. Licensed under MIT.
How do I install io.github.rcsb/rcsb-mcp?: io.github.rcsb/rcsb-mcp supports copy-paste install configs on its MCPpedia page for Claude Desktop, Cursor, and Claude Code. Scroll to the Quick Install section and select your client.
What can io.github.rcsb/rcsb-mcp do?: io.github.rcsb/rcsb-mcp provides 13 tools: sequence, structural, rcsb_search_by_sequence, rcsb_search_by_structure, facets and 8 more. See the full tools list on the server page for descriptions and parameters.
What AI clients work with io.github.rcsb/rcsb-mcp?: io.github.rcsb/rcsb-mcp is compatible with claude-desktop, cursor, claude-code. It uses stdio and sse transport.
Is io.github.rcsb/rcsb-mcp actively maintained?: io.github.rcsb/rcsb-mcp is actively maintained - last commit was 5 days ago. It has 11 GitHub stars.