Legacy Search API Web Service

If your application currently uses Legacy Search API Web Service, it is important that you migrate to the new RCSB PDB Search API so that your application continues to work.

Migration Guidelines Summary:

New Search API specification is not backwards compatible with legacy API.
New Search API returns a JSON response. XML support is discontinued.
New Search API returns identifiers only, no data. You can use a new RCSB PDB Data API service to access the data.
All requests for data should be done through a new RCSB PDB Search API service.

Generic Search Service

Legacy Search API provided a list of preconfigured query options with fixed return type defined by the query type:

Structure-based queries return a list of PDB IDs.
Entity-based queries return a list of PDB IDs appended with entity IDs in the format of pdbid:entityid.
Chain-based query, e.g. Chain ID query. The query result is in the format pdbid:chainid.
Chemical component queries return a list of ligand IDs.

New search system provides flexible search options that can include any combination of fields, available for search. Refer to the Structure Attributes Search and Chemical Attributes Search pages for a full list of searchable fields. Also, return type does not depend on the query type. The following return types are available and can be chosen for any search query:

entry - PDB IDs
polymer_entity, non_polymer_entity - PDB IDs appended with entity IDs in the format of pdbid_entityid
polymer_instance - PDB IDs appended with chain IDs in the format of pdbid.chainid
assembly - PDB IDs appended with assembly IDs in the format of pdbid-assembly

Search for Sequences

Legacy Search API utilized the BLAST method. Former endpoint /pdb/rest/getBlastPDB1. New search system employs MMseqs2 tool. An example of sequence similarity search with protein sequence:

The /pdb/rest/getBlastPDB2 endpoint (BLAST search with Structure ID and Chain ID) is discontinued.

Search for Ligands

The /pdb/rest/smilesQuery endpoint is discontinued. Chemical structure search service is re-implemented using tools from the OpenEye Chemical Toolkit. Chemical search queries are not backward compatible. Please, refer to Search Services documentation to learn more about search options available in the new system.

Contact Us

Contact info@rcsb.org with questions or feedback about this service.