Author: Wang, Yanli; Addess, Kenneth J.; Chen, Jie; Geer, Lewis Y.; He, Jane; He, Siqian; Lu, Shennan; Madej, Thomas; Marchler-Bauer, Aron; Thiessen, Paul A.; Zhang, Naigong; Bryant, Stephen H.
Title: MMDB: annotating protein sequences with Entrez's 3D-structure database Document date: 2006_11_29
ID: 6qpsxmgi_1
Snippet: Experimental three-dimensional (3D) structure data are obtained from the Protein Data Bank (PDB) (2) . Authorannotated features provided by PDB are recorded in MMDB. The agreement between atomic coordinate and sequence data is verified, and sequence data are obtained from PDB coordinate records, if necessary, to resolve ambiguities (3) . Data are mapped into a computer friendly format and transferred between applications using Abstract Syntax Not.....
Document: Experimental three-dimensional (3D) structure data are obtained from the Protein Data Bank (PDB) (2) . Authorannotated features provided by PDB are recorded in MMDB. The agreement between atomic coordinate and sequence data is verified, and sequence data are obtained from PDB coordinate records, if necessary, to resolve ambiguities (3) . Data are mapped into a computer friendly format and transferred between applications using Abstract Syntax Notation 1 (ASN.1). This validation and encoding supports the interoperable display of sequence, structure and alignment. Uniformly defined secondary-structure and 3D-domain features are added to support structure neighbor calculations. MMDB currently contains 39 000 structure entries, corresponding to 90 000 chains and 170 000 3D domains.
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