rcsb API for agents (unofficial) — JSON over curl | clify

RCSB Protein Data Bank (rcsb.org): search 3D macromolecular structures by keyword, attribute or 3D shape, and fetch entry chains, sequence annotations, UniProt alignments, version history, ligand definitions and coordinate/FASTA files.

Host: rcsb.org. Call these verified read commands with plain curl; no install, key, or account. Use the public JSON API with plain curl. No install, key, account, or browser is needed. Example: curl 'https://clify-dev.netlify.app/sites.json'. Start with /search?q=weather, then call /abc/COMMAND. Responses are one JSON object. The hosted MCP and GitHub repo are also available.

Commands

`search-structures`

Full-text keyword search of PDB entries (e.g. 'hemoglobin'), with sorting and offset pagination; returns PDB IDs, titles, methods, organisms and ligands Params: query*, start, rows, sort_by, direction, content_type

curl 'https://clify-dev.netlify.app/rcsb/search-structures'

`search-structures-filtered`

Keyword search of PDB entries refined by one facet filter (source organism, experimental method, etc.), with sorting and pagination Params: query*, filter_attribute, filter_value*, start, rows, sort_by, direction

curl 'https://clify-dev.netlify.app/rcsb/search-structures-filtered'

`search-by-attribute`

Search PDB entries by a structured attribute such as author name, source organism, gene name or experimental method Params: attribute*, value*, operator, start, rows, sort_by, direction

curl 'https://clify-dev.netlify.app/rcsb/search-by-attribute'

`search-similar-assemblies`

3D shape similarity search: find biological assemblies structurally similar to a given entry's assembly Params: entry_id*, assembly_id, operator, start

curl 'https://clify-dev.netlify.app/rcsb/search-similar-assemblies'

`suggest-search-terms`

Autocomplete: suggested search terms (molecule names, keywords, organisms...) for a partial query, grouped by attribute Params: term*

curl 'https://clify-dev.netlify.app/rcsb/suggest-search-terms'

`get-structure-chains`

List the assemblies and polymer chains (entity id, name, label/auth asym ids) of a PDB entry Params: entry_id*

curl 'https://clify-dev.netlify.app/rcsb/get-structure-chains'

`get-entry-instances`

Get all polymer chains of a PDB entry, with molecule names, organisms, sequence lengths, method, resolution and assembly composition (Data API GraphQL) Params: entry_id*

curl 'https://clify-dev.netlify.app/rcsb/get-entry-instances'

`get-entity-instances`

Get the chain instances of one polymer entity (e.g. 4HHB_2), with molecule name, organism, length, method and resolution (Data API GraphQL) Params: entity_ids*

curl 'https://clify-dev.netlify.app/rcsb/get-entity-instances'

`get-sequence-alignment`

Align a PDB entity or chain sequence to its UniProt reference sequence, with coverage and aligned regions (Sequence Coordinates API) Params: queryId*, from, to

curl 'https://clify-dev.netlify.app/rcsb/get-sequence-alignment'

`get-sequence-annotations`

Get positional sequence annotations (Pfam domains, disorder, secondary structure, binding sites, unobserved residues, UniProt features) for a PDB chain or entity Params: queryId*, reference

curl 'https://clify-dev.netlify.app/rcsb/get-sequence-annotations'

`get-structure-summary`

Get the title and IDs of a PDB entry from its structure summary page Params: entry_id*

curl 'https://clify-dev.netlify.app/rcsb/get-structure-summary'

`get-structure-annotations`

List the domain classification rows (SCOP/SCOPe, CATH, ECOD, etc.) for a PDB entry Params: entry_id*

curl 'https://clify-dev.netlify.app/rcsb/get-structure-annotations'

`get-experimental-method`

Get the experimental method (X-ray, EM, NMR...) and experiment page title for a PDB entry Params: entry_id*

curl 'https://clify-dev.netlify.app/rcsb/get-experimental-method'

`list-entry-versions`

List the revision history of a PDB entry (version number, date, change type), with links to versioned files Params: entry_id*

curl 'https://clify-dev.netlify.app/rcsb/list-entry-versions'

`get-entry-fasta`

Download the FASTA sequences of all polymer entities in a PDB entry as text Params: entry_id*

curl 'https://clify-dev.netlify.app/rcsb/get-entry-fasta'

`get-entry-file`

Fetch a PDB entry's coordinate file (mmCIF or legacy PDB) as text, either full or header-only Params: entry_id*, format, part

curl 'https://clify-dev.netlify.app/rcsb/get-entry-file'

`get-ligand-definition`

Get the chemical component definition (name, formula, synonyms, atoms, bonds) of a ligand as mmCIF text, e.g. HEM Params: ligand_id*

curl 'https://clify-dev.netlify.app/rcsb/get-ligand-definition'