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.
The Overview page provides a list of other Web Services offered.
- Get descriptions for the whole PDB file
- Get descriptions for PDB entities
- Get descriptions of chemical components
- Get ligands that are present in a single PDB entry
Lists and status
- Get a PDB ID's release status
- Get a list of all currently released PDB IDs
- Get a list of unreleased PDB IDs
- Get the pre-release sequences in FASTA format
- If there are biological assemblies, get the number of biological assemblies that are available for a PDB ID
- Third-party annotations mapped onto PDB chains
- A PDB to UniProtKB mappings
- Pfam mappings for PDB
- Access Gene Ontology terms for a PDB chain.
Sequence and Structure Clusters
- Sequence and Structure cluster related services
- 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
- Example: List all current PDB IDs in XML: /pdb/rest/getCurrent
- Example: List all current PDB IDs in JSON: /pdb/json/getCurrent
- 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
- 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
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.
- Number of biological assemblies associated with a PDB entry /pdb/rest/bioassembly/nrbioassemblies?structureId=1hv4
- Access the transformation information needed to generate a biological assembly (nr=0 will return information for the asymmetric unit, nr=1 will return information for the first assembly, etc.) /pdb/rest/bioassembly/bioassembly?structureId=1hv4&nr=1
- /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
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.
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/