Web Service APIs: Fetch

RESTful Services support data query and retrieval in both JSON and XML formats. The Web Services mailing list will announce when new APIs are available or updated.

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The Overview page provides a list of other Web Services offered.

Custom Reports


Descriptions


Lists and status


Annotations


Sequence and Structure Clusters



PDB File Description Service
Access general information about a PDB entry (e.g., Header information). Describe the molecular entities that are contained in a PDB entry. Also provides information on the number of available biological assemblies.
Descriptions of PDB entities
Access the descriptions of the entities that are contained in a PDB file.
Descriptions of Chemical Components
Access the descriptions of the chemical components based on their IDs. XML contains a PDB ID as an example of where it can be found.
List all current/obsolete PDB IDs
Get a list of all current PDB IDs. Get a list of all obsolete PDB IDs.
Information about release status
Get Information about the release status for one or multiple PDB ids.
List unreleased PDB IDs
Get a list of PDB IDs that have not been released yet.
List pre-release sequences in FASTA format
Get a list of pre-release sequence in FASTA format.
List biological assemblies

Not all PDB entries have biological assemblies available and some have multiple. Details that are necessary to recreate a biological assembly from the asymmetric unit can be accessed from the following requests.

Ligands in PDB files
List the ligands that can be found in a PDB entry.
Gene Ontology terms for PDB chains
List the Gene Ontology terms that have been annotated for a PDB chain. (Same as on the Annotations tab in the structure explorer pages).
Pfam annotations for PDB entries
The Pfam annotations that are displayed on the RCSB PDB web site are calculated by weekly scripting the Hmmer web site. The calculated annotations can be downloaded using any of these options:
Sequence and Structure cluster related web services
Various requests related to the sequence and 3D - structure clustering are available:

The names of the representative domains are either SCOP domain IDs (starting with "d") or domain IDs as have been assigned with the Protein Domain Parser software ("PDP:")

The all vs. all structural similarity results table for a representative chain can be downloaded in XML. For example, this returns Rank, PDB.Chain, Description, P-value, Score, RMSD, Len1, Len2, %Sim1, and %Sim2 for 3BMV.A /pdb/explorer/structCompXMLData.jsp?method=pw_fatcat&chain=d3bmva1&page=1&rows=10&prettyXML.
Note: A maximum 2000 rows can be returned through this URL. To fetch all approx. 17,000 results for a chain, you need to slice through the results using the page parameter.

There are additional parameters for this URL, which allow sorting. e.g. this sorts by P-value /pdb/explorer/structCompXMLData.jsp?method=pw_fatcat&showAllResults=false&chain=d1iarb1&rows=15&page=1&sidx=probability&sord=asc Parameters that can be used for sorting (the value of the sidx parameter) are: name2,desc,probability, score, rmsdOpt, len1, len2, pid, sim1, sim2.

Third-party annotations and PDB to UniProtKB mapping
DAS Service:
The RESTful services for providing third-party annotations (SCOP, CATH, Pfam, etc.) follows the DAS protocol. The DAS server is available from /pdb/rest/das. The DAS protocol command SOURCES (description of the provided sources) is available from /pdb/rest/das/sources. At the present there are two DAS sources provided:

For more documentation on the DAS protocol, see http://www.dasregistry.org/