TY - JOUR

T1 - ModBase,a database of annotated comparative protein structure models,and associated resources

AU - Pieper, Ursula

AU - Webb, Benjamin M.

AU - Barkan, David T.

AU - Schneidman-Duhovny, Dina

AU - Schlessinger, Avner

AU - Braberg, Hannes

AU - Yang, Zheng

AU - Meng, Elaine C.

AU - Pettersen, Eric F.

AU - Huang, Conrad C.

AU - Datta, Ruchira S.

AU - Sampathkumar, Parthasarathy

AU - Madhusudhan, Mallur S.

AU - Sjölander, Kimmen

AU - Ferrin, Thomas E.

AU - Burley, Stephen K.

AU - Sali, Andrej

N1 - 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).

PY - 2011/1

Y1 - 2011/1

N2 - 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).

AB - 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).

UR - http://www.scopus.com/inward/record.url?scp=78651290702&partnerID=8YFLogxK

U2 - https://doi.org/10.1093/nar/gkq1091

DO - https://doi.org/10.1093/nar/gkq1091

M3 - Article

C2 - 21097780

VL - 39

SP - D465-D474

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - SUPPL. 1

ER -