title: MMDB and VAST+: tracking structural similarities between macromolecular complexes.
abstract: The computational detection of similarities between protein 3D structures has become an indispensable tool for the detection of homologous relationships, the classification of protein families and functional inference. Consequently, numerous algorithms have been developed that facilitate structure comparison, including rapid searches against a steadily growing collection of protein structures. To this end, NCBI's Molecular Modeling Database (MMDB), which is based on the Protein Data Bank (PDB), maintains a comprehensive and up-to-date archive of protein structure similarities computed with the Vector Alignment Search Tool (VAST). These similarities have been recorded on the level of single proteins and protein domains, comprising in excess of 1.5 billion pairwise alignments. Here we present VAST+, an extension to the existing VAST service, which summarizes and presents structural similarity on the level of biological assemblies or macromolecular complexes. VAST+ simplifies structure neighboring results and shows, for macromolecular complexes tracked in MMDB, lists of similar complexes ranked by the extent of similarity. VAST+ replaces the previous VAST service as the default presentation of structure neighboring data in NCBI's Entrez query and retrieval system. MMDB and VAST+ can be accessed via http://www.ncbi.nlm.nih.gov/Structure.
authors: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors: Thomas
authors: T
authors: Madej
authors: Christopher J
authors: CJ
authors: Lanczycki
authors: Dachuan
authors: D
authors: Zhang
authors: Paul A
authors: PA
authors: Thiessen
authors: Renata C
authors: RC
authors: Geer
authors: Aron
authors: A
authors: Marchler-Bauer
authors: Stephen H
authors: SH
authors: Bryant
mesh_terms: D003196:Computer Graphics; D030562:Databases, Protein; D020407:Internet; D046911:Macromolecular Substances / Q000737:chemistry; D008958:Models, Molecular; D012984:Software; D040681:Structural Homology, Protein
chemical_list: D046911:Macromolecular Substances