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

TitleMODBASE: a database of annotated comparative protein structure models and associated resources
Publication TypeJournal Article
Year of Publication2006
AuthorsPieper, U, Eswar, N, Davis, FP, Braberg, H, Madhusudhan, MS, Rossi, A, Marti-Renom, MA, Karchin, R, Webb, BM, Eramian, D, Shen, MY, Kelly, L, Melo, F, Sali, A
JournalNucleic Acids Res
KeywordsBinding Sites *Databases; Molecular Polymorphism; Protein Humans Internet Ligands *Models; Protein Systems Integration User-Computer Interface; Single Nucleotide Protein Structure; Tertiary Proteins/*chemistry/genetics/metabolism Software *Structural Homology

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:/ 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 ( Our other resources integrated with MODBASE include comprehensive databases of multiple protein structure alignments (DBAli,, structurally defined ligand binding sites and structurally defined binary domain interfaces (PIBASE, as well as predictions of ligand binding sites, interactions between yeast proteins, and functional consequences of human nsSNPs (LS-SNP,


Pieper, Ursula Eswar, Narayanan Davis, Fred P Braberg, Hannes Madhusudhan, M S Rossi, Andrea Marti-Renom, Marc Karchin, Rachel Webb, Ben M Eramian, David Shen, Min-Yi Kelly, Libusha Melo, Francisco Sali, Andrej GM 08284/GM/NIGMS NIH HHS/United States P50 GM62529/GM/NIGMS NIH HHS/United States R01 GM 54762/GM/NIGMS NIH HHS/United States R33 CA84699/CA/NCI NIH HHS/United States U54 GM074945/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t England Nucleic acids research Nucleic Acids Res. 2006 Jan 1;34(Database issue):D291-5.