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

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 journal › Article › peer-review

255 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 language	English
Pages (from-to)	D465-D474
Journal	Nucleic Acids Research
Volume	39
Issue number	SUPPL. 1
DOIs	https://doi.org/10.1093/nar/gkq1091
State	Published - Jan 2011
Externally published	Yes

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).

Access to Document

10.1093/nar/gkq1091

Cite this

Pieper, U., Webb, B. M., Barkan, D. T., Schneidman-Duhovny, D., Schlessinger, A., Braberg, H., Yang, Z., Meng, E. C., Pettersen, E. F., Huang, C. C., Datta, R. S., Sampathkumar, P., Madhusudhan, M. S., Sjölander, K., Ferrin, T. E., Burley, S. K., & Sali, A. (2011). ModBase,a database of annotated comparative protein structure models,and associated resources. Nucleic Acids Research, 39(SUPPL. 1), D465-D474. https://doi.org/10.1093/nar/gkq1091

@article{c48046f71035407d91246b9c5c54390f,

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 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).",

author = "Ursula Pieper and Webb, {Benjamin M.} and Barkan, {David T.} and Dina Schneidman-Duhovny and Avner Schlessinger and Hannes Braberg and Zheng Yang and Meng, {Elaine C.} and Pettersen, {Eric F.} and Huang, {Conrad C.} and Datta, {Ruchira S.} and Parthasarathy Sampathkumar and Madhusudhan, {Mallur S.} and Kimmen Sj{\"o}lander and Ferrin, {Thomas E.} and Burley, {Stephen K.} and Andrej Sali",

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).",

year = "2011",

month = jan,

doi = "10.1093/nar/gkq1091",

language = "אנגלית",

volume = "39",

pages = "D465--D474",

journal = "Nucleic Acids Research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "SUPPL. 1",

}

Pieper, U, Webb, BM, Barkan, DT, Schneidman-Duhovny, D, Schlessinger, A, Braberg, H, Yang, Z, Meng, EC, Pettersen, EF, Huang, CC, Datta, RS, Sampathkumar, P, Madhusudhan, MS, Sjölander, K, Ferrin, TE, Burley, SK & Sali, A 2011, 'ModBase,a database of annotated comparative protein structure models,and associated resources', Nucleic Acids Research, vol. 39, no. SUPPL. 1, pp. D465-D474. https://doi.org/10.1093/nar/gkq1091

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 - 10.1093/nar/gkq1091

DO - 10.1093/nar/gkq1091

M3 - ???researchoutput.researchoutputtypes.contributiontojournal.article???

C2 - 21097780

AN - SCOPUS:78651290702

SN - 0305-1048

VL - 39

SP - D465-D474

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - SUPPL. 1

ER -

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

Abstract

Bibliographical note

Access to Document

Other files and links

Fingerprint

Cite this