MMDB: annotating protein sequences with Entrez's 3D-structure database.
Three-dimensional (3D) structure is now known for a large fraction of all protein families. Thus, it has become rather likely that one will find a homolog with known 3D structure when searching a sequence database with an arbitrary query sequence. Depending on the extent of similarity, such neighbor relationships may allow one to infer biological function and to identify functional sites such as binding motifs or catalytic centers. Entrez's 3D-structure database, the Molecular Modeling Database (MMDB), provides easy access to the richness of 3D structure data and its large potential for functional annotation. Entrez's search engine offers several tools to assist biologist users: (i) links between databases, such as between protein sequences and structures, (ii) pre-computed sequence and structure neighbors, (iii) visualization of structure and sequence/structure alignment. Here, we describe an annotation service that combines some of these tools automatically, Entrez's 'Related Structure' links. For all proteins in Entrez, similar sequences with known 3D structure are detected by BLAST and alignments are recorded. The 'Related Structure' service summarizes this information and presents 3D views mapping sequence residues onto all 3D structures available in MMDB (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=structure).
Wang
Yanli
Y
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Addess
Kenneth J
KJ
Chen
Jie
J
Geer
Lewis Y
LY
He
Jane
J
He
Siqian
S
Lu
Shennan
S
Madej
Thomas
T
Marchler-Bauer
Aron
A
Thiessen
Paul A
PA
Zhang
Naigong
N
Bryant
Stephen H
SH
D030562:Databases, Protein; D020407:Internet; D008958:Models, Molecular; D011487:Protein Conformation; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D014584:User-Computer Interface