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Nucleic Acids Research, 2000, Vol. 28, No. 1 243-245
© 2000 Oxford University Press

MMDB: 3D structure data in Entrez

Yanli Wang, Kenneth J. Addess, Lewis Geer, Thomas Madej, Aron Marchler-Bauer, Diane Zimmerman and Stephen H. Bryant*

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

Three-dimensional structures are now known for roughly half of all protein families. It is thus quite likely, in searching sequence databases, that one will encounter a homolog with known structure and be able to use this information to infer structure–function properties. The goal of Entrez’s 3D structure database is to make this information accessible and useful to molecular biologists. To this end, Entrez’s search engine provides three powerful features: (i) Links between databases; one may search by term matching in Medline®, for example, and link to 3D structures reported in these articles. (ii) Sequence and structure neighbors; one may select all sequences similar to one of interest, for example, and link to any known 3D structures. (iii) Sequence and structure visualization; identifying a homolog with known structure, one may view a combined molecular-graphic and alignment display, to infer approximate 3D structure. Entrez’s MMDB (Molecular Modeling DataBase) may be accessed at: http://www.ncbi.nlm.nih.gov/Entrez/structure.html

* To whom correspondence should be addressed. Tel: +1 301 435 7792; Fax: +1 301 480 9241; Email: bryant@ncbi.nlm.nih.gov


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