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Browse the PDB by GO Terms, EC Number, Source Organism, and More
06/07
The RCSB PDB's Browse Database feature can be used to explore the PDB archive using different hierarchical trees. Browsers are available to search for related terms and structures based upon the following classifications:
- Trees for Biological Process, Cellular Component, and Molecular Function are organized using the Gene Ontology (GO) Consortium's descriptions for gene products. PDB IDs and corresponding chain IDs have been mapped to go terms by the SIFTS initiative.
- Enzyme Commission numbers. Search for enzymes by term or by partial or full EC number.
- Membrane Transport proteins organized using Transporter Classification (TC) Database system.
- Source Organism, using organisms found in the NCBI Taxonomy database. These organisms are the source of the individual naturally-occuring polypeptides. The PDB source organism assignment is based on author/UniProtKB specified mapping of polypeptides.
- Genome Location of various organisms. The genomes represented are a subset of the genomes in the NCBI genome database and whose curated sequences for genetic loci are archived at Entrez Gene. The top level in the hierarchy is the organism's genome. Each genome expands into chromosomes which in turn expand into a list of loci on the chomosomes. Each locus is a link to retrieve structures associated with that locus.
- The MeSH (Medical Subject Headings) used to classify publications indexed by the National Library of Medicine, and that appear in the entry's related PubMed abstract.
- SCOP description of evolutionary and functional relationships from SCOP: Structural Classification of Proteins.
- CATH clustering of proteins at 4 major levels from CATH: Protein Structure Classification.
The Browse Database feature can be accessed under the Search widget in the left-hand menu. Each tab links to a different browser.
