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MMDB: 3D structure data in Entrez

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


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.htm

Topics: Article
Publisher: Oxford University Press
Year: 2000
OAI identifier: oai:pubmedcentral.nih.gov:102448
Provided by: PubMed Central
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