MMDB: 3D structure data in Entrez.
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((R)), 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
Wang
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National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Addess
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Geer
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Madej
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Marchler-Bauer
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Zimmerman
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Bryant
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D000595:Amino Acid Sequence; D000818:Animals; D016208:Databases, Factual; D006801:Humans; D016247:Information Storage and Retrieval; D020407:Internet; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017386:Sequence Homology, Amino Acid