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. 2000 Jan 1;28(1):243-5.
doi: 10.1093/nar/28.1.243.

MMDB: 3D structure data in Entrez

Y Wang  1 , K J Addess, L Geer, T Madej, A Marchler-Bauer, D Zimmerman, S H Bryant
Affiliations

MMDB: 3D structure data in Entrez

Y Wang et al. Nucleic Acids Res. .

Abstract

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

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Figures

Figure 1
Figure 1
Connections between MMDB and other databases, including the neighboring mechanisms used to relate entries within the same database.
Figure 2
Figure 2
Cn3D image of the Drosophila paired protein and its alignment with human homeobox protein LMX-1.2. The site of the N→K mutation associated with NPS has been highlighted.
See this image and copyright information in PMC

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