- drawn from PDB
- includes only experimentally resolved structures (i.e., by NMR and X-ray crystallography)
- does not include any theoretical models.
- includes value added information, such as:
- explicit chemical graph showing the bonding between atoms
- atomic substructure classification
- direct 3-D structure comparisons using the VAST (Vector Alignment Search Tool) algorithm to identify structural neighbors
- Links to associated records in other Entrez databases
- PubMed (associated publications)
- Taxonomy (classification of source organism and access to the taxonomic hierarchy)
- Protein (protein sequence records derived from 3-D structure records)
- Nucleotide (nucleotide sequence records derived from 3-D structure records)
- CDD: Conserved Domains (protein domains conserved in molecular evolution)
- 3D Domains (compact structural domains identified by searching for breakpoints in the structure between major secondary structure elements)
- PubChem (links to PubChem for ligands)
- stores records in ASN.1 format; exmaple is shown on next slide.
(background info about ASN.1 is also available, for your reference after the course)
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