title: MMDB: 3D structures and macromolecular interactions.
abstract: Close to 60% of protein sequences tracked in comprehensive databases can be mapped to a known three-dimensional (3D) structure by standard sequence similarity searches. Potentially, a great deal can be learned about proteins or protein families of interest from considering 3D structure, and to this day 3D structure data may remain an underutilized resource. Here we present enhancements in the Molecular Modeling Database (MMDB) and its data presentation, specifically pertaining to biologically relevant complexes and molecular interactions. MMDB is tightly integrated with NCBI's Entrez search and retrieval system, and mirrors the contents of the Protein Data Bank. It links protein 3D structure data with sequence data, sequence classification resources and PubChem, a repository of small-molecule chemical structures and their biological activities, facilitating access to 3D structure data not only for structural biologists, but also for molecular biologists and chemists. MMDB provides a complete set of detailed and pre-computed structural alignments obtained with the VAST algorithm, and provides visualization tools for 3D structure and structure/sequence alignment via the molecular graphics viewer Cn3D. MMDB can be accessed at http://www.ncbi.nlm.nih.gov/structure.
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA. madej@ncbi.nlm.nih.gov
authors.forename: Thomas
authors.initials: T
authors.lastname: Madej
authors.forename: Kenneth J
authors.initials: KJ
authors.lastname: Addess
authors.forename: Jessica H
authors.initials: JH
authors.lastname: Fong
authors.forename: Lewis Y
authors.initials: LY
authors.lastname: Geer
authors.forename: Renata C
authors.initials: RC
authors.lastname: Geer
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Lanczycki
authors.forename: Chunlei
authors.initials: C
authors.lastname: Liu
authors.forename: Shennan
authors.initials: S
authors.lastname: Lu
authors.forename: Aron
authors.initials: A
authors.lastname: Marchler-Bauer
authors.forename: Anna R
authors.initials: AR
authors.lastname: Panchenko
authors.forename: Jie
authors.initials: J
authors.lastname: Chen
authors.forename: Paul A
authors.initials: PA
authors.lastname: Thiessen
authors.forename: Yanli
authors.initials: Y
authors.lastname: Wang
authors.forename: Dachuan
authors.initials: D
authors.lastname: Zhang
authors.forename: Stephen H
authors.initials: SH
authors.lastname: Bryant
mesh_terms: D030562:Databases, Protein; D008958:Models, Molecular; D011487:Protein Conformation; D020539:Sequence Analysis, Protein