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

Research output: Contribution to journalArticle

215 Citations (Scopus)

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 languageEnglish (US)
JournalNucleic Acids Research
Volume39
Issue numberSUPPL. 1
DOIs
StatePublished - Jan 2011
Externally publishedYes

Fingerprint

Databases
Sequence Alignment
Proteins
X-Rays
Peptides

ASJC Scopus subject areas

  • Genetics

Cite this

Pieper, U., Webb, B. M., Barkan, D. T., Schneidman-Duhovny, D., Schlessinger, A., Braberg, H., ... Sali, A. (2011). ModBase,a database of annotated comparative protein structure models,and associated resources. Nucleic Acids Research, 39(SUPPL. 1). https://doi.org/10.1093/nar/gkq1091

ModBase,a database of annotated comparative protein structure models,and associated resources. / Pieper, Ursula; Webb, Benjamin M.; Barkan, David T.; Schneidman-Duhovny, Dina; Schlessinger, Avner; Braberg, Hannes; Yang, Zheng; Meng, Elaine C.; Pettersen, Eric F.; Huang, Conrad C.; Datta, Ruchira S.; Sampathkumar, Parthasarathy; Madhusudhan, Mallur S.; Sjölander, Kimmen; Ferrin, Thomas E.; Burley, Stephen K.; Sali, Andrej.

In: Nucleic Acids Research, Vol. 39, No. SUPPL. 1, 01.2011.

Research output: Contribution to journalArticle

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. https://doi.org/10.1093/nar/gkq1091
Pieper U, Webb BM, Barkan DT, Schneidman-Duhovny D, Schlessinger A, Braberg H et al. ModBase,a database of annotated comparative protein structure models,and associated resources. Nucleic Acids Research. 2011 Jan;39(SUPPL. 1). https://doi.org/10.1093/nar/gkq1091
Pieper, Ursula ; Webb, Benjamin M. ; Barkan, David T. ; Schneidman-Duhovny, Dina ; Schlessinger, Avner ; Braberg, Hannes ; Yang, Zheng ; Meng, Elaine C. ; Pettersen, Eric F. ; Huang, Conrad C. ; Datta, Ruchira S. ; Sampathkumar, Parthasarathy ; Madhusudhan, Mallur S. ; Sjölander, Kimmen ; Ferrin, Thomas E. ; Burley, Stephen K. ; Sali, Andrej. / ModBase,a database of annotated comparative protein structure models,and associated resources. In: Nucleic Acids Research. 2011 ; Vol. 39, No. SUPPL. 1.
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