Sequence Similarity Search
science.pdb.sequenceRead-onlyIdempotent
Find PDB structures matching a protein sequence using BLAST. Configure identity cutoff and E-value to retrieve homologous chains for homology modeling and structure prediction.
Instructions
Search protein structures by amino acid sequence similarity (BLAST). Input a protein sequence and find all PDB structures with matching chains. Configure identity cutoff (e.g. 90%) and E-value threshold. Returns PDB entity IDs ranked by similarity score. Essential for homology modeling and structure prediction (RCSB PDB)
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| sequence | Yes | Protein amino acid sequence in one-letter code (e.g. "MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSH" — first 50 residues of human hemoglobin alpha) | |
| identity_cutoff | No | Minimum sequence identity (0.1-1.0). Default: 0.9 (90% identical) | |
| evalue_cutoff | No | Maximum E-value threshold for BLAST significance. Default: 0.1 | |
| limit | No | Maximum number of results (1-50). Default: 10 |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| result | No | Tool response payload. Shape varies per tool — consult the tool description and inputSchema. May be an object, array, string, or number depending on the upstream provider response. | |
| error | No | Present only when the call failed. Includes error code, message, request_id, and any provider-specific extras. |