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*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

250 Scopus citations

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).

Original languageAmerican English
Pages (from-to)D465-D474
JournalNucleic Acids Research
Volume39
Issue numberSUPPL. 1
DOIs
StatePublished - Jan 2011
Externally publishedYes

Bibliographical note

Funding Information:
National Institutes of Health (R01 GM54762, U54 GM074945, U54 GM074929, U01 GM61390, P01 GM71790 to A.S., F32 GM088991 to A.Sch., P41 RR001081 to T.E.F.); the National Science Foundation (0732065 to A.S. and K.S.); the Department of Energy (DE-SC0004916 to K.S.); Sandler Family Supporting Foundation (to A.S). Funding for open access charge: NIH (U54 GM074945).

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