Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (265K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Pieper, U.
Right arrow Articles by Sali, A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Pieper, U.
Right arrow Articles by Sali, A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2004, Vol. 32, Database issue D217-D222
© 2004 Oxford University Press

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

Ursula Pieper, Narayanan Eswar, Hannes Braberg, M. S. Madhusudhan, Fred P. Davis, Ashley C. Stuart1, Nebojsa Mirkovic1, Andrea Rossi, Marc A. Marti-Renom, Andras Fiser2, Ben Webb, Daniel Greenblatt, Conrad C. Huang, Thomas E. Ferrin and Andrej Sali*

Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research, Mission Bay Genentech Hall, 600 16th Street, Suite N472D, University of California San Francisco, San Francisco, CA 94143-2240, USA, 1 Laboratory of Molecular Biophysics, Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University, New York, NY 10021, USA and 2 Department of Biochemistry and Seaver Foundation Center for Bioinformatics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA

*To whom correspondence should be addressed. Tel: +1 415 514 4227; Fax: +1 415 514 4231; Email: sali{at}salilab.org

MODBASE (http://salilab.org/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on the MODELLER package for fold assignment, sequence–structure alignment, model building and model assessment (http:/salilab.org/modeller). MODBASE uses the MySQL relational database management system for flexible querying and CHIMERA for viewing the sequences and structures (http://www.cgl.ucsf.edu/chimera/). MODBASE is updated regularly to reflect the growth in protein sequence and structure databases, as well as improvements in the software for calculating the models. For ease of access, MODBASE is organized into different data sets. The largest data set contains 1 262 629 models for domains in 659 495 out of 1 182 126 unique protein sequences in the complete Swiss-Prot/TrEMBL database (August 25, 2003); only models based on alignments with significant similarity scores and models assessed to have the correct fold despite insignificant alignments are included. Another model data set supports target selection and structure-based annotation by the New York Structural Genomics Research Consortium; e.g. the 53 new structures produced by the consortium allowed us to characterize structurally 24 113 sequences. MODBASE also contains binding site predictions for small ligands and a set of predicted interactions between pairs of modeled sequences from the same genome. Our other resources associated with MODBASE include a comprehensive database of multiple protein structure alignments (DBALI, http://salilab.org/dbali) as well as web servers for automated comparative modeling with MODPIPE (MODWEB, http://salilab. org/modweb), modeling of loops in protein structures (MODLOOP, http://salilab.org/modloop) and predicting functional consequences of single nucleotide polymorphisms (SNPWEB, http://salilab. org/snpweb).


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 MicrobiologyHome page
D. Ruiz, P. Salinas, M. L. Lopez-Redondo, M. L. Cayuela, A. Marina, and A. Contreras
Phosphorylation-independent activation of the atypical response regulator NblR
Microbiology, October 1, 2008; 154(10): 3002 - 3015.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
E. G. Minguet, F. Vera-Sirera, A. Marina, J. Carbonell, and M. A. Blazquez
Evolutionary Diversification in Polyamine Biosynthesis
Mol. Biol. Evol., October 1, 2008; 25(10): 2119 - 2128.
[Abstract] [Full Text] [PDF]

Home page
 Protein Sci.Home page
P. Larsson, B. Wallner, E. Lindahl, and A. Elofsson
Using multiple templates to improve quality of homology models in automated homology modeling
Protein Sci., June 1, 2008; 17(6): 990 - 1002.
[Abstract] [Full Text] [PDF]

Home page
 J Child NeurolHome page
J. Maletkovic, R. Schiffmann, J. R. Gorospe, E. S. Gordon, M. Mintz, E. P. Hoffman, G. Alper, D. R. Lynch, B. S. Singhal, C. Harding, et al.
Genetic and Clinical Heterogeneity in eIF2B-Related Disorder
J Child Neurol, February 1, 2008; 23(2): 205 - 215.
[Abstract] [PDF]

Home page
 Biophys. JHome page
H. Chen and J. Skolnick
M-TASSER: An Algorithm for Protein Quaternary Structure Prediction
Biophys. J., February 1, 2008; 94(3): 918 - 928.
[Abstract] [Full Text] [PDF]

Home page
 Protein Eng Des SelHome page
V. Pabuwal and Z. Li
Network pattern of residue packing in helical membrane proteins and its application in membrane protein structure prediction
Protein Eng. Des. Sel., January 3, 2008; (2008) gzm059v1.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
C. L. Naessan, W. Egge-Jacobsen, R. W. Heiniger, M. C. Wolfgang, F. E. Aas, A. Rohr, H. C. Winther-Larsen, and M. Koomey
Genetic and Functional Analyses of PptA, a Phospho-Form Transferase Targeting Type IV Pili in Neisseria gonorrhoeae
J. Bacteriol., January 1, 2008; 190(1): 387 - 400.
[Abstract] [Full Text] [PDF]

Home page
 Hum Mol GenetHome page
K. A. Beaumont, S. L. Shekar, R. A. Newton, M. R. James, J. L. Stow, D. L. Duffy, and R. A. Sturm
Receptor function, dominant negative activity and phenotype correlations for MC1R variant alleles
Hum. Mol. Genet., September 15, 2007; 16(18): 2249 - 2260.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
H. Zhou and J. Skolnick
Ab Initio Protein Structure Prediction Using Chunk-TASSER
Biophys. J., September 1, 2007; 93(5): 1510 - 1518.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
R. Nijland, R. Heerlien, L. W. Hamoen, and O. P. Kuipers
Changing a Single Amino Acid in Clostridium perfringens {beta}-Toxin Affects the Efficiency of Heterologous Secretion by Bacillus subtilis
Appl. Envir. Microbiol., March 1, 2007; 73(5): 1586 - 1593.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. J. Cockell, B. Oliva, and R. M. Jackson
Structure-based evaluation of in silico predictions of protein protein interactions using Comparative Docking
Bioinformatics, March 1, 2007; 23(5): 573 - 581.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
N. J. Mulder, R. Apweiler, T. K. Attwood, A. Bairoch, A. Bateman, D. Binns, P. Bork, V. Buillard, L. Cerutti, R. Copley, et al.
New developments in the InterPro database
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D224 - D228.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
W. Zhang, Y. Zhang, H. Zheng, C. Zhang, W. Xiong, J. G. Olyarchuk, M. Walker, W. Xu, M. Zhao, S. Zhao, et al.
SynDB: a Synapse protein DataBase based on synapse ontology
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D737 - D741.
[Abstract] [Full Text] [PDF]

Home page
 Protein Sci.Home page
S. Martinez-Rodriguez, M. Andujar-Sanchez, J. L. Neira, J. M. Clemente-Jimenez, V. Jara-Perez, F. Rodriguez-Vico, and F. J. Las Heras-Vazquez
Site-directed mutagenesis indicates an important role of cysteines 76 and 181 in the catalysis of hydantoin racemase from Sinorhizobium meliloti
Protein Sci., December 1, 2006; 15(12): 2729 - 2738.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
N. Fernandez-Fuentes, J. Zhai, and A. Fiser
ArchPRED: a template based loop structure prediction server.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W173 - W176.
[Abstract] [Full Text] [PDF]

Home page
 Protein Sci.Home page
D. Eramian, M.-y. Shen, D. Devos, F. Melo, A. Sali, and M. A. Marti-Renom
A composite score for predicting errors in protein structure models
Protein Sci., July 1, 2006; 15(7): 1653 - 1666.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
F. Hsu, W. J. Kent, H. Clawson, R. M. Kuhn, M. Diekhans, and D. Haussler
The UCSC Known Genes
Bioinformatics, May 1, 2006; 22(9): 1036 - 1046.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
U. Pieper, N. Eswar, F. P. Davis, H. Braberg, M. S. Madhusudhan, A. Rossi, M. Marti-Renom, R. Karchin, B. M. Webb, D. Eramian, et al.
MODBASE: a database of annotated comparative protein structure models and associated resources
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D291 - D295.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T. Castrignano, P. D. De Meo, D. Cozzetto, I. G. Talamo, and A. Tramontano
The PMDB Protein Model Database
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D306 - D309.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Kopp and T. Schwede
The SWISS-MODEL Repository: new features and functionalities
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D315 - D318.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
K. L. Schneider, K. S. Pollard, R. Baertsch, A. Pohl, and T. M. Lowe
The UCSC Archaeal Genome Browser
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D407 - D410.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. S. Hinrichs, D. Karolchik, R. Baertsch, G. P. Barber, G. Bejerano, H. Clawson, M. Diekhans, T. S. Furey, R. A. Harte, F. Hsu, et al.
The UCSC Genome Browser Database: update 2006
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D590 - D598.
[Abstract] [Full Text] [PDF]

Home page
 Protein Sci.Home page
D. Korkin, F. P. Davis, and A. Sali
Localization of protein-binding sites within families of proteins
Protein Sci., September 1, 2005; 14(9): 2350 - 2360.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
R. Karchin, M. Diekhans, L. Kelly, D. J. Thomas, U. Pieper, N. Eswar, D. Haussler, and A. Sali
LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources
Bioinformatics, June 15, 2005; 21(12): 2814 - 2820.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
J. Espadaler, R. Aragues, N. Eswar, M. A. Marti-Renom, E. Querol, F. X. Aviles, A. Sali, and B. Oliva
Detecting remotely related proteins by their interactions and sequence similarity
PNAS, May 17, 2005; 102(20): 7151 - 7156.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
W.J. Kent, F. Hsu, D. Karolchik, R. M. Kuhn, H. Clawson, H. Trumbower, and D. Haussler
Exploring relationships and mining data with the UCSC Gene Sorter
Genome Res., May 1, 2005; 15(5): 737 - 741.
[Abstract] [Full Text] [PDF]

Home page
 Protein Sci.Home page
B. Wallner and A. Elofsson
All are not equal: A benchmark of different homology modeling programs
Protein Sci., May 1, 2005; 14(5): 1315 - 1327.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
F. P. Davis and A. Sali
PIBASE: a comprehensive database of structurally defined protein interfaces
Bioinformatics, May 1, 2005; 21(9): 1901 - 1907.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
F. Hsu, T. H. Pringle, R. M. Kuhn, D. Karolchik, M. Diekhans, D. Haussler, and W. J. Kent
The UCSC Proteome Browser
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D454 - D458.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
M. R. Chance, A. Fiser, A. Sali, U. Pieper, N. Eswar, G. Xu, J. E. Fajardo, T. Radhakannan, and N. Marinkovic
High-Throughput Computational and Experimental Techniques in Structural Genomics
Genome Res., October 1, 2004; 14(10b): 2145 - 2154.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Liu and B. Rost
Sequence-based prediction of protein domains
Nucleic Acids Res., July 7, 2004; 32(12): 3522 - 3530.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.