title: MODBASE: a database of annotated comparative protein structure models and associated resources.
abstract: MODBASE (http://salilab.org/modbase) is a database of annotated comparative protein structure models for all available protein sequences that can be matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on MODELLER for fold assignment, sequence-structure alignment, model building and model assessment (http:/salilab.org/modeller). MODBASE is updated regularly to reflect the growth in protein sequence and structure databases, and improvements in the software for calculating the models. MODBASE currently contains 3 094 524 reliable models for domains in 1 094 750 out of 1 817 889 unique protein sequences in the UniProt database (July 5, 2005); only models based on statistically significant alignments and models assessed to have the correct fold despite insignificant alignments are included. MODBASE also allows users to generate comparative models for proteins of interest with the automated modeling server MODWEB (http://salilab.org/modweb). Our other resources integrated with MODBASE include comprehensive databases of multiple protein structure alignments (DBAli, http://salilab.org/dbali), structurally defined ligand binding sites and structurally defined binary domain interfaces (PIBASE, http://salilab.org/pibase) as well as predictions of ligand binding sites, interactions between yeast proteins, and functional consequences of human nsSNPs (LS-SNP, http://salilab.org/LS-SNP).
authors.affiliation: Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, QB3 at Mission Bay, Office 503B, University of California at San Francisco 1700 4th Street, San Francisco, CA 94158, USA.
authors.forename: Ursula
authors.initials: U
authors.lastname: Pieper
authors.forename: Narayanan
authors.initials: N
authors.lastname: Eswar
authors.forename: Fred P
authors.initials: FP
authors.lastname: Davis
authors.forename: Hannes
authors.initials: H
authors.lastname: Braberg
authors.forename: M S
authors.initials: MS
authors.lastname: Madhusudhan
authors.forename: Andrea
authors.initials: A
authors.lastname: Rossi
authors.forename: Marc
authors.initials: M
authors.lastname: Marti-Renom
authors.forename: Rachel
authors.initials: R
authors.lastname: Karchin
authors.forename: Ben M
authors.initials: BM
authors.lastname: Webb
authors.forename: David
authors.initials: D
authors.lastname: Eramian
authors.forename: Min-Yi
authors.initials: MY
authors.lastname: Shen
authors.forename: Libusha
authors.initials: L
authors.lastname: Kelly
authors.forename: Francisco
authors.initials: F
authors.lastname: Melo
authors.forename: Andrej
authors.initials: A
authors.lastname: Sali
mesh_terms: D001665:Binding Sites; D030562:Databases, Protein; D006801:Humans; D020407:Internet; D008024:Ligands; D008958:Models, Molecular; D020641:Polymorphism, Single Nucleotide; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012984:Software; D040681:Structural Homology, Protein; D018511:Systems Integration; D014584:User-Computer Interface
chemical_list: D008024:Ligands; D011506:Proteins