rcsb_search_by_seqmotif
Find RCSB PDB polymer entities (proteins, DNA, RNA) that contain a specific sequence motif using PROSITE, regex, or simple wildcard patterns, and retrieve matching structure IDs with scores.
Instructions
Find polymers containing a short sequence motif (PROSITE / regex / simple).
Args:
pattern: The motif, e.g. "C-x(2,4)-C-x(3)-[LIVMFYWC]-x(8)-H-x(3,5)-H"
(prosite), "C..H[LIVF]" (regex), or "NXS" (simple wildcards).
pattern_type: "prosite" (default), "regex", or "simple".
sequence_type: "protein" (default), "dna", or "rna".
return_type: What to return (default "polymer_entity"); see the "Return types and
fetching details" note in the server instructions.
limit: Max hits (1-100).
offset: Number of hits to skip, for paging; pass the response's next_offset back with
the same query to fetch the next page.
all_hits: Return the COMPLETE result set in one call (for an explicit "ALL ..." request);
ignores limit, can't be combined with offset, and is refused above 10000 hits.
Ignored when facets is set.
attributes: Optional structured filters AND/OR-combined with this match — a list of
AttributeFilter {attribute, operator, value, negation?, case_sensitive?} (e.g.
restrict to an organism or resolution). See rcsb_search_by_attribute /
rcsb_list_pdb_search_attributes for paths and operators.
logical_operator: Combine this match and the attribute conditions with "and"
(default) or "or".
facets: Optional aggregation specs to return a breakdown / distribution instead of hits
(see the faceting note in the server instructions for the spec).
group_by, group_by_ranking: Collapse redundant polymer_entity hits into clusters, one
representative each (needs return_type="polymer_entity") — see the grouping note in
the server instructions.
sort_by: Attribute path to order the hits by, replacing the default score ordering (each
hit's score is still returned); omit to keep it. Only SORTABLE attributes work: those
listing exact_match (strings) or equals (numbers/dates) in
rcsb_list_pdb_search_attributes; full-text-only attributes (e.g. struct.title) and
return_type="mol_definition" are rejected.
sort_direction: "asc" (default) or "desc"; applies only when sort_by is set.
Returns:
{total_count, returned, offset, has_more, next_offset, hits:[{id, score}],
editor}; with facets, instead returns {total_count, facets, editor}.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| limit | No | ||
| facets | No | ||
| offset | No | ||
| pattern | Yes | ||
| sort_by | No | ||
| all_hits | No | ||
| group_by | No | ||
| attributes | No | ||
| return_type | No | polymer_entity | |
| pattern_type | No | prosite | |
| sequence_type | No | protein | |
| sort_direction | No | asc | |
| group_by_ranking | No | ||
| logical_operator | No | and |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||