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

Ursula Pieper, 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

Research output: Contribution to journalArticle

204 Scopus citations

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).

Original languageEnglish (US)
Pages (from-to)D291-295
JournalNucleic acids research
Volume34
Issue numberDatabase issue
StatePublished - Jan 1 2006
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

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    Pieper, U., Eswar, N., Davis, F. P., Braberg, H., Madhusudhan, M. S., Rossi, A., Marti-Renom, M., Karchin, R., Webb, B. M., Eramian, D., Shen, M. Y., Kelly, L., Melo, F., & Sali, A. (2006). MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic acids research, 34(Database issue), D291-295.