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

Ursula Pieper (1) , Benjamin M. Webb (1) , Guang Qiang Dong (1) , Dina Schneidman-Duhovny (1) , Hao Fan (1) , Seung Joong Kim (1) , Natalia Khuri (1, 2) , Yannick G. Spill (3, 4) , Patrick Weinkam (1) , Michal Hammel (5) , John A. Tainer (6, 5) , Michael Nilges (3) , Andrej Sali (1)

1 Department of Bioengineering and Therapeutic Sciences
2 Graduate Group in Biophysics
3 Bioinformatique structurale - Structural Bioinformatics
4 UPD7 - Université Paris Diderot - Paris 7
5 LBNL - Lawrence Berkeley National Laboratory [Berkeley]
6 Department of Chemistry

ModBase (http://salilab.org/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 (http://salilab.org/modeller/). 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 (http://salilab.org/ modweb). ModBase models are also available through the Protein Model Portal (http://www.prote inmodelportal.org/). Recently developed associated resources include the AllosMod server for modeling ligand-induced protein dynamics (http://salilab.org/ allosmod), the AllosMod-FoXS server for predicting a structural ensemble that fits an SAXS profile (http://salilab.org/allosmod-foxs), the FoXSDock server for protein–protein docking filtered by an SAXS profile (http://salilab.org/foxsdock), the SAXS Merge server for automatic merging of SAXS profiles (http://salilab.org/saxsmerge) and the Pose & Rank server for scoring protein–ligand complexes (http://salilab.org/poseandrank). 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.

Domains: Life Sciences [q-bio]; Quantitative Methods [q-bio.QM]

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⟩