The RCSB PDB RESTful Web Service interface

Access general information about a PDB entry (e.g., Header information).

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

Describe the molecular entities that are contained in a PDB entry. Also provides information on the number of available biological assemblies.

• Example: Access for one PDB ID/pdb/rest/getEntityInfo?structureId=1hv4
• Example: Access the information for all PDB IDs: /pdb/rest/getEntityInfo

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

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

Get a list of all current PDB IDs.

• Example: List all current PDB IDs: /pdb/rest/getCurrent

Get a list of all obsolete PDB IDs.

• Example: List all obsolete PDB IDs: /pdb/rest/getObsolete

BLAST with Sequence.

• Example: HTML output: /pdb/rest/getBlastPDB1?sequence=VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTAVAHVDDMPNAL&eCutOff=10.0&matrix=BLOSUM62&outputFormat=HTML
• Example: XML output: /pdb/rest/getBlastPDB1?sequence=VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTAVAHVDDMPNAL&eCutOff=10.0&matrix=BLOSUM62&outputFormat=XML
• Example: Plain text output: /pdb/rest/getBlastPDB1?sequence=VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTAVAHVDDMPNAL&eCutOff=10.0&matrix=BLOSUM62

BLAST with Structure ID and Chain ID.

• Example: HTML output: /pdb/rest/getBlastPDB2?structureId=4HHB&chainId=A&eCutOff=10.0&matrix=BLOSUM62&outputFormat=HTML
• Example: XML output: /pdb/rest/getBlastPDB2?structureId=4HHB&chainId=A&eCutOff=10.0&matrix=BLOSUM62&outputFormat=XML
• Example: Plain text output: /pdb/rest/getBlastPDB2?structureId=4HHB&chainId=A&eCutOff=10.0&matrix=BLOSUM62

View a Java example that submits a BLAST search via a POST: PostBLASTQuery.java

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

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
• Example: Access the information of unreleased PDB IDs based on SG Project Initials: /pdb/rest/getUnreleased?sgInit=SSGCID

Get a list of pre-release sequence in FASTA format.

• Example: Access the information for a subset of PDB IDs: /pdb/rest/getStatusSequence?structureId=3MU6,3QV1,3SSF
• Example: Access the information for a subset of PDB IDs, entity type, and range of deposition date: /pdb/rest/getStatusSequence?entityType=RNA&depositionDateMin=2011-07-01&depositionDateMax=2011-07-30 (The entity type can be RNA, DNA, and Polypeptide.)
• Example: Access the information for all unreleased PDB IDs: /pdb/rest/getStatusSequence

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

• Example: /pdb/rest/ligandInfo?structureId=4HHB

List the Gene Ontology terms that have been annotated for a PDB chain. (Same as on the Annotations 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

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:

• per PDB ID: /pdb/rest/hmmer?structureId=4hhb
• all annotations in one XML file /pdb/rest/hmmer
• all annotations in one tab-delimited file /pdb/rest/hmmer?file=hmmer_pdb_all.txt

View a Javascript example that displays a simple 3D view of a structure using PV.

• Example: pv_symmetry.jsp

Various requests related to the sequence and 3D - structure clustering are available:

• /pdb/rest/sequenceCluster?cluster=40&structureId=4hhb.A Get all the sequence cluster at 40% sequence ID for a particular chain ID.
• /pdb/rest/representatives?cluster=40 Get all representative chains from the 40% sequence clustering.
• /pdb/rest/representatives?structureId=4hhb.A Get the representative for a chain (the chain on Rank 1 in the sequence clustering).
• /pdb/rest/representativeDomains?cluster=40 Get all representative domains that are used for the systematic structure alignments.
• /pdb/rest/representativeDomains?structureId=4hhb.A Get the representatives domains for a chain.

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.

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/

This query performs chemical structure searches using SMILES and SMARTS linear notations.
Search types include exact, substructure, superstructure and similarity.

• Exact: find an exact structure match
  
/pdb/rest/smilesQuery?smiles=NC(=O)C1=CC=CC=C1&search_type=exact
• Substructure: find ligands that contain the specified structure as a substructure
  
/pdb/rest/smilesQuery?smiles=NC(=O)C1=CC=CC=C1&search_type=substructure

• Superstructure: find ligands that are substructures (fragments) of the specified structure
  
/pdb/rest/smilesQuery?smiles=OC(=O)c1ccc(OCc2ccccc2)cc1&search_type=superstructure

• Similarity: find structures that bind similar ligands.
  Specify a similarity threshold to change the degree of similarity in the [0...1] range: 0 dissimilar ... 1 identical.
  The similarity is based on the number of chemical features in common between the query and the target molecule. Similarity is calculated using the Tanimoto Coefficient.
/pdb/rest/smilesQuery?smiles=OC(=O)c1ccc(OCc2ccccc2)cc1&search_type=similarity&similarity=0.7

This interface exposes the RCSB PDB advanced search interface as an XML Web Service.

To use 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 top of the page is 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: