title: MODBASE, a database of annotated comparative protein structure models, and associated resources.
abstract: MODBASE (http://salilab.org/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on the MODELLER package for fold assignment, sequence-structure alignment, model building and model assessment (http:/salilab.org/modeller). MODBASE uses the MySQL relational database management system for flexible querying and CHIMERA for viewing the sequences and structures (http://www.cgl.ucsf.edu/chimera/). MODBASE is updated regularly to reflect the growth in protein sequence and structure databases, as well as improvements in the software for calculating the models. For ease of access, MODBASE is organized into different data sets. The largest data set contains 1,26,629 models for domains in 659,495 out of 1,182,126 unique protein sequences in the complete Swiss-Prot/TrEMBL database (August 25, 2003); only models based on alignments with significant similarity scores and models assessed to have the correct fold despite insignificant alignments are included. Another model data set supports target selection and structure-based annotation by the New York Structural Genomics Research Consortium; e.g. the 53 new structures produced by the consortium allowed us to characterize structurally 24,113 sequences. MODBASE also contains binding site predictions for small ligands and a set of predicted interactions between pairs of modeled sequences from the same genome. Our other resources associated with MODBASE include a comprehensive database of multiple protein structure alignments (DBALI, http://salilab.org/dbali) as well as web servers for automated comparative modeling with MODPIPE (MODWEB, http://salilab. org/modweb), modeling of loops in protein structures (MODLOOP, http://salilab.org/modloop) and predicting functional consequences of single nucleotide polymorphisms (SNPWEB, http://salilab. org/snpweb).
authors.affiliation: Department of Biopharmaceutical Sciences, and California Institute for Quantitative Biomedical Research, Mission Bay Genentech Hall, 600 16th Street, Suite N472D, University of California San Francisco, San Francisco, CA 94143-2240, USA.
authors.forename: Ursula
authors.initials: U
authors.lastname: Pieper
authors.forename: Narayanan
authors.initials: N
authors.lastname: Eswar
authors.forename: Hannes
authors.initials: H
authors.lastname: Braberg
authors.forename: M S
authors.initials: MS
authors.lastname: Madhusudhan
authors.forename: Fred P
authors.initials: FP
authors.lastname: Davis
authors.forename: Ashley C
authors.initials: AC
authors.lastname: Stuart
authors.forename: Nebojsa
authors.initials: N
authors.lastname: Mirkovic
authors.forename: Andrea
authors.initials: A
authors.lastname: Rossi
authors.forename: Marc A
authors.initials: MA
authors.lastname: Marti-Renom
authors.forename: Andras
authors.initials: A
authors.lastname: Fiser
authors.forename: Ben
authors.initials: B
authors.lastname: Webb
authors.forename: Daniel
authors.initials: D
authors.lastname: Greenblatt
authors.forename: Conrad C
authors.initials: CC
authors.lastname: Huang
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Ferrin
authors.forename: Andrej
authors.initials: A
authors.lastname: Sali
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D019295:Computational Biology; D030562:Databases, Protein; D023281:Genomics; D006801:Humans; D020407:Internet; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D016415:Sequence Alignment; D012984:Software; D014584:User-Computer Interface
chemical_list: D008024:Ligands; D011506:Proteins