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PMID: 18948282 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

MODBASE, a database of annotated comparative protein structure models and associated resources.

Nucleic acids research ·Vol. 37 ·No. Database issue ·2009-01-00 ·Pages D347-54

Pieper U, Eswar N, Webb BM, Eramian D, Kelly L, Barkan DT, Carter H, Mankoo P, Karchin R, Marti-Renom MA, Davis FP, Sali A

Abstract

MODBASE (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by MODPIPE, an automated modeling pipeline that relies primarily on MODELLER for fold assignment, sequence-structure alignment, model building and model assessment (http:/salilab.org/modeller). MODBASE currently contains 5,152,695 reliable models for domains in 1,593,209 unique protein sequences; only models based on statistically significant alignments and/or models assessed to have the correct fold are included. MODBASE also allows users to calculate comparative models on demand, through an interface to the MODWEB modeling server (http://salilab.org/modweb). Other resources integrated with MODBASE include databases of multiple protein structure alignments (DBAli), structurally defined ligand binding sites (LIGBASE), predicted ligand binding sites (AnnoLyze), structurally defined binary domain interfaces (PIBASE) and annotated single nucleotide polymorphisms and somatic mutations found in human proteins (LS-SNP, LS-Mut). MODBASE models are also available through the Protein Model Portal (http://www.proteinmodelportal.org/).

MeSH Terms
Databases, Protein Genomics Humans Ligands Models, Molecular Mutation Polymorphism, Single Nucleotide Protein Folding Protein Interaction Domains and Motifs Protein Structure, Tertiary Proteins/genetics Structural Homology, Protein User-Computer Interface
Chemicals
Ligands Proteins
Authors & Affiliations
12 authors, click to expand affiliations / ORCID
Pieper Ursula
Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, USA.
Eswar Narayanan
Webb Ben M
Eramian David
Kelly Libusha
Barkan David T
Carter Hannah
Mankoo Parminder
Karchin Rachel
Marti-Renom Marc A
Davis Fred P
Sali Andrej
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkn791
Published
2009-01-00
Epub
2008-00-23
Pages
D347-54
Language
English
Region
England
NLM ID
0411011
PMCID
PMC2686492
Subset
IM
Grants
NIGMS NIH HHS · U01 GM61390 · United States
NIGMS NIH HHS · R01 GM54762 · United States
NIGMS NIH HHS · GM08284 · United States
NIGMS NIH HHS · P01 GM71790 · United States
NIGMS NIH HHS · U54 GM074945 · United States
NIGMS NIH HHS · U54 GM074929 · United States
External Links
PubMed source DOI: 10.1093/nar/gkn791 PMC Full Text View journal details
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