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

Ursula Pieper, Benjamin M. Webb, Guang Qiang Dong, Dina Schneidman-Duhovny, Hao Fan, Seung Joong Kim, Natalia Khuri, Yannick G. Spill, Patrick Weinkam, Michal Hammel, John A. Tainer, Michael Nilges, Andrej Sali*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

241 Scopus citations


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 ( ModBase currently contains almost 30 million reliable models for domains in 4.7 million unique protein sequences. ModBase allows users to compute or update comparative models on demand, through an interface to the ModWeb modeling server ( ModBase models are also available through the Protein Model Portal (http://www. Recently developed associated resources include the AllosMod server for modeling ligand-induced protein dynamics (, the AllosMod-FoXS server for predicting a structural ensemble that fits an SAXS profile ( , the FoXSDock server for protein-protein docking filtered by an SAXS profile (, the SAXS Merge server for automatic merging of SAXS profiles ( and the Pose & Rank server for scoring protein-ligand complexes ( In this update, we also highlight two applications of ModBase: a PSI:Biology initiative to maximize the structural coverage of the human alpha-helical transmembrane proteome and a determination of structural determinants of human immunodeficiency virus-1 protease specificity.

Original languageAmerican English
Pages (from-to)D336-D346
JournalNucleic Acids Research
Issue numberD1
StatePublished - 1 Jan 2014
Externally publishedYes

Bibliographical note

Funding Information:
National Institutes of Health [U54 GM094662, U54 GM094625, U54 GM093342, MINOS R01GM105404 to J.A.T. and M.H.]; Sandler Family Supporting Foundation (A.S.); Department of Energy Lawrence Berkeley National Lab IDAT program (to J.A.T. and M.H.); European Union [FP7-IDEAS-ERC 294809 to M.N.]. The authors thank Tom Ferrin and the UCSF Resource for Biocomputing, Visualization and Informatics for making UCSF Chimera (supported by [NIGMS P41-GM103311]) available to the ModBase database and tools. Funding for open access charge: NIH.


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