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The RCSB PDB RESTful Web Service interface

The RCSB PDB is supporting RESTful (REpresentational State Transfer) Web Services to make accessing data easier. Please use these services instead of screen-scraping. If relevant services are missing, please let us know.

As a general strategy we are trying to implement two types of services for our RESTful interface:

Search services: to return a list of IDs (i.e. PDB IDs, chain IDs, ligand IDs)
Fetch services: to return data given a ID

At the present the following services are provided:

SEARCH services

A generic SEARCH service allowing to POST advanced queries
Search for Ligands and PDB IDs based on a SMILES query

FETCH services

View descriptions for the whole PDB file
View descriptions for PDB entities
View descriptions of chemical components
Get information about the release status of a PDB ID
Get a list of unreleased PDB IDs
Viewing Ligands that are present in a single protein structure
A service for providing third-party annotations mapped onto PDB chains
A service for accessing PDB to UniProtKB mappings
Access Gene Ontology terms for a PDB chain.

Descriptions of PDB entities:

PDB File Description Service:

Access overall descriptions of the PDB file.

Example: Show the information for one file: /pdb/rest/describePDB?structureId=4hhb
Example: Show the information for multiple files: /pdb/rest/describePDB?structureId=4hhb,1hhb

Descriptions of PDB entities:

Entity Description Service:

Access the descriptions of the entities that are contained in a PDB file.

Example: Access the information for all entities in the file: /pdb/rest/describeMol?structureId=4hhb
Example: Access the information only for a single PDB chain: /pdb/rest/describeMol?structureId=4hhb.A

Descriptions of Chemical Components:

Chemical Component Description Service:

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.

Example: Access the information for one components: /pdb/rest/describeHet?chemicalID=NAG
Example: Access the information for multiple components: /pdb/rest/describeHet?chemicalID=NAG,EBW

Information about release status:

Release Status Service:

Get Information about the release status for one or multiple PDB ids.

Example: Access the information for a one PDB ID: /pdb/rest/idStatus?structureId=4HHB
Example: Access the information for a set of PDB IDs: /pdb/rest/idStatus?structureId=450D,451D

List unreleased PDB IDs:

Description Service:

Get a list of PDB IDs that have not been released yet.

Example: Access the information for a subset of PDB IDs: /pdb/rest/getUnreleased?structureId=450D,451D
Example: Access the information for all unreleased PDB IDs: /pdb/rest/getUnreleased

Ligands in PDB files:

LigandInfo Service:

List the ligands that can be found in a PDB entry.

Example: /pdb/rest/ligandInfo?structureId=4hhb

Gene Ontology terms for PDB chains:

Gene Ontology Service:

List the Gene Ontology terms that have been annotated for a PDB chain. (Same as on the Derived Data tab in the structure explorer pages).

Example: /pdb/rest/goTerms?structureId=4hhb
Example: /pdb/rest/goTerms?structureId=4hhb.A
Example: /pdb/rest/goTerms?structureId=4hhb.A,1a4w.H

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:

pdbchainfeatures:
Provides various third party annotations that have been computed for PDB chains.
Get the third party features (a DAS - FEATURES request): /pdb/rest/das/pdbchainfeatures/features?segment=5pti.A
Get the ATOM sequence of the PDB chain (a DAS - SEQUENCE request): /pdb/rest/das/pdbchainfeatures/sequence?segment=5pti.A
pdb_uniprot_mapping:
Provides a DAS source that is serving the alignment between UniProtKB and PDB, derived from the SIFTS mappings.
Example: Get all alignments for a PDB (a DAS - ALIGNMENT request) /pdb/rest/das/pdb_uniprot_mapping/alignment?query=4hhb
Example: Get all alignments for a single PDB chain (a DAS - ALIGNMENT request) /pdb/rest/das/pdb_uniprot_mapping/alignment?query=4hhb.A

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

Search PDB with SMILES string:

SMILES search:

Lists the ligands and PDB IDs that match a SMILES query.

Example1: /pdb/rest/smilesQuery?smiles=[I-]&dissimilarity=0.3&search_type=3
Search for SMILES string "[I-]". The dissimilarity score is set to 0.3 The search type is 3 (that is the constant from JChemSearch.SIMILARITY).
Example2: /pdb/rest/smilesQuery?smiles=CN(C)c1cccc2c1cccc2S(=O)(=O)O&dissimilarity=0.3&search_type=3
(longer SMILES string)

SEARCH service:

SEARCH service:

At present this interface exposes the RCSB PDB advanced search interface as an XML Web Service.

In order to utilize this service, POST a XML representation of an advanced search to /pdb/rest/search.

XML representation of advanced search

Every advanced search can be represented by XML. To view an example representation, simply execute an advanced search query and then click on the Result tab. One of the links on the left hand menu is Show Query Details. Clicking on this link will provide the XML representation of the query.

Every query is described by two data items:

queryType: the name of the class that is implementing the query
arguments: depending on the type of query that is being executed one or more differently named arguments need to be provided.

Sample XML Queries:

The Query is displayed in the Textbox below

Example:

<orgPdbQuery>    
    <queryType>org.pdb.query.simple.UpAccessionIdQuery</queryType>
    <description>Simple query for a list of UniprotKB Accession IDs: P50225</description>   
    <accessionIdList>P50225</accessionIdList>
</orgPdbQuery>

Now let's POST this query against the Web Service:

Results will go here:

Examples:

View a Perl example that submits a simple search for organism: search_organism.pl
View a Java example that submits a more complex Advanced Search doing a BLAST search and only looking at X-RAY structures. PostXMLQuery.java
View a Python example that submits a simple search for all Solid State NMR proteins: search_nmr.py

The RCSB PDB is managed by two members of the RCSB:
Rutgers and UCSD, and is funded by NSF, NIGMS, DOE, NLM, NCI, NINDS, and NIDDK.