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

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

doi:10.1093/nar/gkt1144

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

Abstract

ModBase (http://salilab.org/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://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 comparative 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 transmembrane proteome and a determination of structural determinants of human immunodeficiency virus-1 protease specificity.

Authors:

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

Univ. of California, San Francisco, CA (United States)
Instiut Pasteur, Paris (France). Structural Bioinformatics Unit. Structural Biology and Chemistry Dept.; Universite Paris Diderot-Paris (France)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
The Scripps Research Inst., La Jolla, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Instiut Pasteur, Paris (France). Structural Bioinformatics Unit. Structural Biology and Chemistry Dept.

Publication Date:: Sat Nov 23 00:00:00 EST 2013

Research Org.:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

OSTI Identifier:: 1625516

Grant/Contract Number:: AC02-05CH11231

Resource Type:: Accepted Manuscript

Journal Name:: Nucleic Acids Research

Additional Journal Information:: Journal Volume: 42; Journal Issue: D1; Journal ID: ISSN 0305-1048

Publisher:: Oxford University Press

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; Biochemistry & Molecular Biology

Citation Formats


                    Pieper, Ursula, Webb, Benjamin M., Dong, Guang Qiang, Schneidman-Duhovny, Dina, Fan, Hao, Kim, Seung Joong, Khuri, Natalia, Spill, Yannick G., Weinkam, Patrick, Hammel, Michal, Tainer, John A., Nilges, Michael, and Sali, Andrej. ModBase, a database of annotated comparative protein structure models and associated resources.  United States: N. p., 2013. 
Web.  doi:10.1093/nar/gkt1144.

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                    Pieper, Ursula, Webb, Benjamin M., Dong, Guang Qiang, Schneidman-Duhovny, Dina, Fan, Hao, Kim, Seung Joong, Khuri, Natalia, Spill, Yannick G., Weinkam, Patrick, Hammel, Michal, Tainer, John A., Nilges, Michael, & Sali, Andrej. ModBase, a database of annotated comparative protein structure models and associated resources.  United States.  https://doi.org/10.1093/nar/gkt1144

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                    Pieper, Ursula, Webb, Benjamin M., Dong, Guang Qiang, Schneidman-Duhovny, Dina, Fan, Hao, Kim, Seung Joong, Khuri, Natalia, Spill, Yannick G., Weinkam, Patrick, Hammel, Michal, Tainer, John A., Nilges, Michael, and Sali, Andrej. Sat .  
"ModBase, a database of annotated comparative protein structure models and associated resources".  United States.  https://doi.org/10.1093/nar/gkt1144.  https://www.osti.gov/servlets/purl/1625516.

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@article{osti_1625516,

  title        = {ModBase, a database of annotated comparative protein structure models and associated resources},

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

  abstractNote = {ModBase (http://salilab.org/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://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 comparative 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 transmembrane proteome and a determination of structural determinants of human immunodeficiency virus-1 protease specificity.},

  doi          = {10.1093/nar/gkt1144},

  journal      = {Nucleic Acids Research},

  number       = D1,

  volume       = 42,

  place        = {United States},

  year         = {Sat Nov 23 00:00:00 EST 2013},

  month        = {Sat Nov 23 00:00:00 EST 2013}

}

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