{"ok":true,"site":"rcsb","host":"rcsb.org","about":"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.","commands":[{"command":"search-structures","summary":"Full-text keyword search of PDB entries (e.g. 'hemoglobin'), with sorting and offset pagination; returns PDB IDs, titles, methods, organisms and ligands","params":[{"name":"query","type":"string","required":true,"description":"Free-text search terms"},{"name":"start","type":"number","description":"0-based result offset. Use 25 for page 2.","default":0},{"name":"rows","type":"number","description":"Results per page","default":25},{"name":"sort_by","type":"string","description":"Sort key: relevance score or initial release date","oneOf":["score","rcsb_accession_info.initial_release_date"],"default":"score"},{"name":"direction","type":"string","description":"Sort direction. Use desc with the release date to get the newest entries first.","oneOf":["desc","asc"],"default":"desc"},{"name":"content_type","type":"string","description":"experimental = PDB entries; computational = computed structure models (CSM)","oneOf":["experimental","computational"],"default":"experimental"}],"exampleUrl":"https://clify-dev.netlify.app/rcsb/search-structures"},{"command":"search-structures-filtered","summary":"Keyword search of PDB entries refined by one facet filter (source organism, experimental method, etc.), with sorting and pagination","params":[{"name":"query","type":"string","required":true,"description":"Free-text search terms"},{"name":"filter_attribute","type":"string","description":"Facet attribute to refine on (exact match)","oneOf":["rcsb_entity_source_organism.ncbi_scientific_name","exptl.method","rcsb_entry_info.polymer_entity_count_protein","struct_keywords.pdbx_keywords"],"default":"rcsb_entity_source_organism.ncbi_scientific_name"},{"name":"filter_value","type":"string","required":true,"description":"Exact facet value, e.g. 'Homo sapiens' for organism, or 'X-RAY DIFFRACTION', 'ELECTRON MICROSCOPY' or 'SOLUTION NMR' for exptl.method"},{"name":"start","type":"number","description":"0-based result offset","default":0},{"name":"rows","type":"number","description":"Results per page","default":25},{"name":"sort_by","type":"string","description":"Sort key","oneOf":["score","rcsb_accession_info.initial_release_date"],"default":"score"},{"name":"direction","type":"string","description":"Sort direction","oneOf":["desc","asc"],"default":"desc"}],"exampleUrl":"https://clify-dev.netlify.app/rcsb/search-structures-filtered"},{"command":"search-by-attribute","summary":"Search PDB entries by a structured attribute such as author name, source organism, gene name or experimental method","params":[{"name":"attribute","type":"string","required":true,"description":"Search attribute path. Examples: audit_author.name, rcsb_entity_source_organism.ncbi_scientific_name, rcsb_entity_source_organism.rcsb_gene_name.value, exptl.method, struct.title"},{"name":"value","type":"string","required":true,"description":"Value to match, e.g. 'HBB', 'Perutz, M.F.' or 'Homo sapiens'"},{"name":"operator","type":"string","description":"Comparison operator","oneOf":["exact_match","contains_phrase","contains_words","in","exists"],"default":"exact_match"},{"name":"start","type":"number","description":"0-based result offset","default":0},{"name":"rows","type":"number","description":"Results per page","default":25},{"name":"sort_by","type":"string","description":"Sort key","oneOf":["score","rcsb_accession_info.initial_release_date"],"default":"score"},{"name":"direction","type":"string","description":"Sort direction","oneOf":["desc","asc"],"default":"desc"}],"exampleUrl":"https://clify-dev.netlify.app/rcsb/search-by-attribute"},{"command":"search-similar-assemblies","summary":"3D shape similarity search: find biological assemblies structurally similar to a given entry's assembly","params":[{"name":"entry_id","type":"string","required":true,"description":"PDB ID of the query structure"},{"name":"assembly_id","type":"string","description":"Assembly ID of the query structure (see get-structure-chains)","default":"1"},{"name":"operator","type":"string","description":"Shape match strictness","oneOf":["strict_shape_match","relaxed_shape_match"],"default":"strict_shape_match"},{"name":"start","type":"number","description":"0-based result offset","default":0}],"exampleUrl":"https://clify-dev.netlify.app/rcsb/search-similar-assemblies"},{"command":"suggest-search-terms","summary":"Autocomplete: suggested search terms (molecule names, keywords, organisms...) for a partial query, grouped by attribute","params":[{"name":"term","type":"string","required":true,"description":"Partial search text"}],"exampleUrl":"https://clify-dev.netlify.app/rcsb/suggest-search-terms"},{"command":"get-structure-chains","summary":"List the assemblies and polymer chains (entity id, name, label/auth asym ids) of a PDB entry","params":[{"name":"entry_id","type":"string","required":true,"description":"PDB ID, e.g. 4HHB"}],"exampleUrl":"https://clify-dev.netlify.app/rcsb/get-structure-chains"},{"command":"get-entry-instances","summary":"Get all polymer chains of a PDB entry, with molecule names, organisms, sequence lengths, method, resolution and assembly composition (Data API GraphQL)","params":[{"name":"entry_id","type":"string","required":true,"description":"PDB ID, e.g. 4HHB"}],"exampleUrl":"https://clify-dev.netlify.app/rcsb/get-entry-instances"},{"command":"get-entity-instances","summary":"Get the chain instances of one polymer entity (e.g. 4HHB_2), with molecule name, organism, length, method and resolution (Data API GraphQL)","params":[{"name":"entity_ids","type":"string","required":true,"description":"Polymer entity ID in the form <PDBID>_<entity number>, e.g. 4HHB_1"}],"exampleUrl":"https://clify-dev.netlify.app/rcsb/get-entity-instances"},{"command":"get-sequence-alignment","summary":"Align a PDB entity or chain sequence to its UniProt reference sequence, with coverage and aligned regions (Sequence Coordinates API)","params":[{"name":"queryId","type":"string","required":true,"description":"Entity ID (4HHB_2) when from=PDB_ENTITY, or chain instance ID (4HHB.B) when from=PDB_INSTANCE"},{"name":"from","type":"string","description":"Sequence reference type of queryId","oneOf":["PDB_ENTITY","PDB_INSTANCE","UNIPROT"],"default":"PDB_ENTITY"},{"name":"to","type":"string","description":"Target sequence reference","oneOf":["UNIPROT","PDB_ENTITY","PDB_INSTANCE"],"default":"UNIPROT"}],"exampleUrl":"https://clify-dev.netlify.app/rcsb/get-sequence-alignment"},{"command":"get-sequence-annotations","summary":"Get positional sequence annotations (Pfam domains, disorder, secondary structure, binding sites, unobserved residues, UniProt features) for a PDB chain or entity","params":[{"name":"queryId","type":"string","required":true,"description":"Chain instance ID (4HHB.B) when reference=PDB_INSTANCE, or entity ID (4HHB_2) when reference=PDB_ENTITY"},{"name":"reference","type":"string","description":"Coordinate system of queryId","oneOf":["PDB_INSTANCE","PDB_ENTITY","UNIPROT"],"default":"PDB_INSTANCE"}],"exampleUrl":"https://clify-dev.netlify.app/rcsb/get-sequence-annotations"},{"command":"get-structure-summary","summary":"Get the title and IDs of a PDB entry from its structure summary page","params":[{"name":"entry_id","type":"string","required":true,"description":"PDB ID, e.g. 4HHB"}],"exampleUrl":"https://clify-dev.netlify.app/rcsb/get-structure-summary"},{"command":"get-structure-annotations","summary":"List the domain classification rows (SCOP/SCOPe, CATH, ECOD, etc.) for a PDB entry","params":[{"name":"entry_id","type":"string","required":true,"description":"PDB ID"}],"exampleUrl":"https://clify-dev.netlify.app/rcsb/get-structure-annotations"},{"command":"get-experimental-method","summary":"Get the experimental method (X-ray, EM, NMR...) and experiment page title for a PDB entry","params":[{"name":"entry_id","type":"string","required":true,"description":"PDB ID"}],"exampleUrl":"https://clify-dev.netlify.app/rcsb/get-experimental-method"},{"command":"list-entry-versions","summary":"List the revision history of a PDB entry (version number, date, change type), with links to versioned files","params":[{"name":"entry_id","type":"string","required":true,"description":"PDB ID"}],"exampleUrl":"https://clify-dev.netlify.app/rcsb/list-entry-versions"},{"command":"get-entry-fasta","summary":"Download the FASTA sequences of all polymer entities in a PDB entry as text","params":[{"name":"entry_id","type":"string","required":true,"description":"PDB ID"}],"exampleUrl":"https://clify-dev.netlify.app/rcsb/get-entry-fasta"},{"command":"get-entry-file","summary":"Fetch a PDB entry's coordinate file (mmCIF or legacy PDB) as text, either full or header-only","params":[{"name":"entry_id","type":"string","required":true,"description":"PDB ID"},{"name":"format","type":"string","description":"File format","oneOf":["cif","pdb"],"default":"cif"},{"name":"part","type":"string","description":"header = metadata only (small); view = full coordinates (can be large)","oneOf":["header","view"],"default":"header"}],"exampleUrl":"https://clify-dev.netlify.app/rcsb/get-entry-file"},{"command":"get-ligand-definition","summary":"Get the chemical component definition (name, formula, synonyms, atoms, bonds) of a ligand as mmCIF text, e.g. HEM","params":[{"name":"ligand_id","type":"string","required":true,"description":"Chemical component ID (1-5 chars), e.g. HEM, ATP, NAG"}],"exampleUrl":"https://clify-dev.netlify.app/rcsb/get-ligand-definition"}]}