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

Ursula Pieper; Benjamin M Webb; David T Barkan; Dina Schneidman-Duhovny; Avner Schlessinger; Hannes Braberg; Zheng Yang; Elaine C Meng; Eric F Pettersen; Conrad C Huang; Ruchira S Datta; Parthasarathy Sampathkumar; Mallur S Madhusudhan; Kimmen Sjölander; Thomas E Ferrin; Stephen K Burley; Andrej Sali

doi:10.1093/nar/gkq1091

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

Journal article

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

Ursula Pieper, Benjamin M Webb, David T Barkan, Dina Schneidman-Duhovny, Avner Schlessinger, Hannes Braberg, Zheng Yang, Elaine C Meng, Eric F Pettersen, Conrad C Huang, …

Nucleic acids research, Vol.39(Database issue), pp.D465-D474

01/2011

DOI: https://doi.org/10.1093/nar/gkq1091

PMCID: PMC3013688

PMID: 21097780

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 10 355 444 reliable models for domains in 2 421 920 unique protein sequences. ModBase allows users to update comparative models on demand, and request modeling of additional sequences through an interface to the ModWeb modeling server ( http://salilab.org/modweb ). ModBase models are available through the ModBase interface as well as the Protein Model Portal ( http://www.proteinmodelportal.org/ ). Recently developed associated resources include the SALIGN server for multiple sequence and structure alignment ( http://salilab.org/salign ), the ModEval server for predicting the accuracy of protein structure models ( http://salilab.org/modeval ), the PCSS server for predicting which peptides bind to a given protein ( http://salilab.org/pcss ) and the FoXS server for calculating and fitting Small Angle X-ray Scattering profiles ( http://salilab.org/foxs ).

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Title: ModBase, a database of annotated comparative protein structure models, and associated resources
Creators: Ursula Pieper - Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California at San Francisco, CA 94158
Benjamin M Webb - Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California at San Francisco, CA 94158
David T Barkan - Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California at San Francisco, CA 94158
Dina Schneidman-Duhovny - Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California at San Francisco, CA 94158
Avner Schlessinger - Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California at San Francisco, CA 94158
Hannes Braberg - Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California at San Francisco, CA 94158
Zheng Yang - Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California at San Francisco, CA 94158
Elaine C Meng - Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California at San Francisco, CA 94158
Eric F Pettersen - Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California at San Francisco, CA 94158
Conrad C Huang - Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California at San Francisco, CA 94158
Ruchira S Datta - Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California at San Francisco, CA 94158
Parthasarathy Sampathkumar - Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California at San Francisco, CA 94158
Mallur S Madhusudhan - Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California at San Francisco, CA 94158
Kimmen Sjölander - Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California at San Francisco, CA 94158
Thomas E Ferrin - Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California at San Francisco, CA 94158
Stephen K Burley - Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California at San Francisco, CA 94158
Andrej Sali - Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California at San Francisco, CA 94158
Publication Details: Nucleic acids research, Vol.39(Database issue), pp.D465-D474
Date published: 01/2011
Publisher: Oxford University Press
Academic Unit: Chemistry and Chemical Biology (SAS); Institute for Quantitative Biomedicine
Language: English
Resource Type: Journal article
Identifiers: 991031666095004646