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

Abstract : ModBase ( is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an auto- mated 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 com- parative models on demand, through an interface to the ModWeb modeling server ( modweb). ModBase models are also available through the Protein Model Portal (http://www.prote Recently developed associated resources include the AllosMod server for modeling ligand-induced protein dynamics ( allosmod), 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 transmem- brane proteome and a determination of structural determinants of human immunodeficiency virus-1 protease specificity.
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Submitted on : Monday, December 12, 2016 - 11:05:19 AM
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Ursula Pieper, Benjamin M. Webb, Guang Qiang Dong, Dina Schneidman-Duhovny, Hao Fan, et al.. ModBase, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Research, 2013, 42 (D1), pp.D336 - D346. ⟨10.1093/nar/gkt1144⟩. ⟨pasteur-01414232⟩



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