MMDB: annotating protein sequences with Entrez's 3D-structure database

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.

The 'Related Structure' service is also integrated with NCBI's protein BLAST service. A 'Related Structures' link is provided when one or more similar proteins with known 3D structures have been identified by BLAST. The NCBI single-nucleotide polymorphism resource (SNP) also links to the 'Related Structure' service, which in this context provides a mapping of both synonymous and non-synonymous coding SNPs onto experimentally determined 3D structures. 'Related Structure' may be expanded further in the future, to provide visualization for other NCBI resources and to support additional filtering and selection among related structures, e.g. to highlight those annotated with conserved domain footprints by the CDD resource or those linked to small molecules in the PubChem database. Figure 3 . A Cn3D view of the query sequence from Figure 2 aligned to chain A of the related structure 1O86 (PDB code). Residues in aligned regions are displayed in upper case letters with identical residue pairs rendered in red color. Residues within a 5 A contact radius of the bound drug lisinopril are highlighted in the 3D structure view and automatically mapped onto the aligned residues shown in the sequence alignment window. Side chains of these residues are displayed selectively and rendered as ball-andstick models.