MODBASE: a database of annotated comparative protein structure models and associated resources - PubMed (original) (raw)

. 2006 Jan 1;34(Database issue):D291-5.

doi: 10.1093/nar/gkj059.

Narayanan Eswar, Fred P Davis, Hannes Braberg, M S Madhusudhan, Andrea Rossi, Marc Marti-Renom, Rachel Karchin, Ben M Webb, David Eramian, Min-Yi Shen, Libusha Kelly, Francisco Melo, Andrej Sali

Affiliations

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

Ursula Pieper et al. Nucleic Acids Res. 2006.

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).

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Figures

Figure 1

Figure 1

MODBASE Model Details page (example S15435468 from the Grape-1 dataset): This page provides links to all models for a specific sequence. A ribbon diagram of the primary model, database annotations and modeling details are displayed. Links to additional models for different target regions or models from other datasets are displayed as thumbprints. The pull-down menu provides access to alternative MODBASE views and other types of information (if available), such as data about SNPs and putative ligand binding sites.

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