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 Publication2009
AuthorsPieper, U, Eswar, N, Webb, BM, Eramian, D, Kelly, L, Barkan, DT, Carter, H, Mankoo, P, Karchin, R, Marti-Renom, MA, Davis, FP, Sali, A
JournalNucleic Acids Res
Keywords*Databases; Molecular Mutation Polymorphism; Protein Genomics Humans Ligands *Models; Protein User-Computer Interface; Single Nucleotide Protein Folding Protein Interaction Domains and Motifs *Protein Structure; Tertiary Proteins/genetics *Structural Homology

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:/ 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 ( 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 (


Pieper, Ursula 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 GM08284/GM/NIGMS NIH HHS/United States P01 GM71790/GM/NIGMS NIH HHS/United States R01 GM54762/GM/NIGMS NIH HHS/United States U01 GM61390/GM/NIGMS NIH HHS/United States U54 GM074929/GM/NIGMS 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 Research Support, U.S. Gov’t, Non-P.H.S. England Nucleic acids research Nucleic Acids Res. 2009 Jan;37(Database issue):D347-54. Epub 2008 Oct 23.