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Nucleic Acids Research Advance Access originally published online on November 29, 2006
Nucleic Acids Research 2007 35(Database issue):D298-D300; doi:10.1093/nar/gkl952
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Nucleic Acids Research, 2007, Vol. 35, Database issue D298-D300
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

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

Yanli Wang, Kenneth J. Addess, Jie Chen, Lewis Y. Geer, Jane He, Siqian He, Shennan Lu, Thomas Madej, Aron Marchler-Bauer, Paul A. Thiessen, Naigong Zhang and Stephen H. Bryant*

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20894, USA

*To whom correspondence should be addressed. Tel: +1 301 435 7792; Fax: +1 301 435 7793; Email: bryant{at}ncbi.nlm.nih.gov

Received September 20, 2006. Revised October 17, 2006. Accepted October 20, 2006.

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).


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A comparative view at comprehensive information resources on three-dimensional structures of biological macro-molecules
Brief Funct Genomic Proteomic, October 23, 2007; (2007) elm020v1.
[Abstract] [Full Text] [PDF]


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