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PMID: 21097780 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

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

Nucleic acids research ·Vol. 39 ·No. Database issue ·2011-01-00 ·Pages D465-74

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

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).

MeSH Terms
Bacterial Proteins/chemistry Computer Graphics Databases, Protein Models, Molecular Peptides/chemistry Protein Interaction Mapping Protein Structure, Tertiary Proteins/chemistry Scattering, Small Angle Sequence Alignment Software Structural Homology, Protein User-Computer Interface X-Ray Diffraction
Chemicals
Bacterial Proteins Peptides Proteins
Authors & Affiliations
17 authors, click to expand affiliations / ORCID
Pieper Ursula
Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California at San Francisco, CA 94158, USA.
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
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkq1091
Published
2011-01-00
Epub
2010-00-19
Pages
D465-74
Language
English
Region
England
NLM ID
0411011
PMCID
PMC3013688
Subset
IM
Grants
NIGMS NIH HHS · U01 GM61390 · United States
NIGMS NIH HHS · R01 GM54762 · United States
NIGMS NIH HHS · P01GM71790 · United States
NIGMS NIH HHS · U54 GM074945 · United States
NCRR NIH HHS · P41RR001081 · United States
NIGMS NIH HHS · U54GM074945 · United States
NIGMS NIH HHS · F32 GM088991 · United States
NIGMS NIH HHS · U54 GM074929 · United States
External Links
PubMed source DOI: 10.1093/nar/gkq1091 PMC Full Text View journal details
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