title: MMDB: Entrez's 3D-structure database.
abstract: Three-dimensional structures are now known within many protein families and it is quite likely, in searching a sequence database, that one will encounter a homolog with known structure. The goal of Entrez's 3D-structure database is to make this information, and the functional annotation it can provide, easily accessible to molecular biologists. To this end Entrez's search engine provides three powerful features. (i) Sequence and structure neighbors; one may select all sequences similar to one of interest, for example, and link to any known 3D structures. (ii) Links between databases; one may search by term matching in MEDLINE, for example, and link to 3D structures reported in these articles. (iii) Sequence and structure visualization; identifying a homolog with known structure, one may view molecular-graphic and alignment displays, to infer approximate 3D structure. In this article we focus on two features of Entrez's Molecular Modeling Database (MMDB) not described previously: links from individual biopolymer chains within 3D structures to a systematic taxonomy of organisms represented in molecular databases, and links from individual chains (and compact 3D domains within them) to structure neighbors, other chains (and 3D domains) with similar 3D structure. MMDB may be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure.
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
authors.forename: Yanli
authors.initials: Y
authors.lastname: Wang
authors.forename: John B
authors.initials: JB
authors.lastname: Anderson
authors.forename: Jie
authors.initials: J
authors.lastname: Chen
authors.forename: Lewis Y
authors.initials: LY
authors.lastname: Geer
authors.forename: Siqian
authors.initials: S
authors.lastname: He
authors.forename: David I
authors.initials: DI
authors.lastname: Hurwitz
authors.forename: Cynthia A
authors.initials: CA
authors.lastname: Liebert
authors.forename: Thomas
authors.initials: T
authors.lastname: Madej
authors.forename: Gabriele H
authors.initials: GH
authors.lastname: Marchler
authors.forename: Aron
authors.initials: A
authors.lastname: Marchler-Bauer
authors.forename: Anna R
authors.initials: AR
authors.lastname: Panchenko
authors.forename: Benjamin A
authors.initials: BA
authors.lastname: Shoemaker
authors.forename: James S
authors.initials: JS
authors.lastname: Song
authors.forename: Paul A
authors.initials: PA
authors.lastname: Thiessen
authors.forename: Roxanne A
authors.initials: RA
authors.lastname: Yamashita
authors.forename: Stephen H
authors.initials: SH
authors.lastname: Bryant
mesh_terms: D000818:Animals; D003196:Computer Graphics; D030562:Databases, Protein; D006801:Humans; D021621:Imaging, Three-Dimensional; D016247:Information Storage and Retrieval; D020407:Internet; D009317:National Library of Medicine (U.S.); D010802:Phylogeny; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D014481:United States
chemical_list: D011506:Proteins