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MODBASE, a database of annotated comparative protein structure models

R. Sanchez
2000 Nucleic Acids Research  
MODBASE is a queryable database of annotated comparative protein structure models. The models are derived by MODPIPE, an automated modeling pipeline relying on the programs PSI-BLAST and MODELLER.  ...  The database currently contains 3D models for substantial portions of approximately 17 000 proteins from 10 complete genomes, including those of Caenorhabditis elegans, Saccharomyces cerevisiae and Escherichia  ...  ACKNOWLEDGEMENTS We are grateful to Dr Steve A. Chervitz for making links from Sacch3D to MODBASE, and to Dr Ashley Stuart for comments on the manuscript.  ... 
doi:10.1093/nar/28.1.250 pmid:10592238 pmcid:PMC102433 fatcat:igjppda6uzftnctbum4qr7tpmy

MODBASE, a database of annotated comparative protein structure models

U. Pieper
2002 Nucleic Acids Research  
MODBASE is a queryable database of annotated comparative protein structure models. The models are derived by MODPIPE, an automated modeling pipeline relying on the programs PSI-BLAST and MODELLER.  ...  The database currently contains 3D models for substantial portions of approximately 17 000 proteins from 10 complete genomes, including those of Caenorhabditis elegans, Saccharomyces cerevisiae and Escherichia  ...  ACKNOWLEDGEMENTS We are grateful to Dr Steve A. Chervitz for making links from Sacch3D to MODBASE, and to Dr Ashley Stuart for comments on the manuscript.  ... 
doi:10.1093/nar/30.1.255 pmid:11752309 pmcid:PMC99112 fatcat:h7ux4rhukreidjsu7af7nbgigy

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

U. Pieper
2004 Nucleic Acids Research  
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  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkh095 pmid:14681398 pmcid:PMC308829 fatcat:blq5hwxzh5gobc32e6c5y3gu6a

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

U. Pieper
2006 Nucleic Acids Research  
MODBASE (http://salilab.org/modbase) is a database of annotated comparative protein structure models for all available protein sequences that can be matched to at least one known protein structure.  ...  MODBASE also allows users to generate comparative models for proteins of interest with the automated modeling server MODWEB (http://salilab.org/modweb).  ...  For linking to MODBASE from their databases, we thank David Haussler, Jim Kent (UCSC Genome Browser), Amos Bairoch (SwissProt/TrEMBL), Rolf Apweiler (InterPro), Patsy Babbitt (SFLD), and Kathy Wu (PIR/  ... 
doi:10.1093/nar/gkj059 pmid:16381869 pmcid:PMC1347422 fatcat:quimgf3kibesrcsogatfoeizp4

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

Ursula Pieper, Benjamin M. Webb, Guang Qiang Dong, Dina Schneidman-Duhovny, Hao Fan, Seung Joong Kim, Natalia Khuri, Yannick G. Spill, Patrick Weinkam, Michal Hammel, John A. Tainer, Michael Nilges (+1 others)
2013 Nucleic Acids Research  
MODBASE (http://salilab.org/modbase) is a database of annotated comparative protein structure models.  ...  MODBASE also allows users to calculate comparative models on demand, through an interface to the MODWEB modeling server  ...  ACKNOWLEDGEMENTS We are grateful to Tom Ferrin, Daniel Greenblatt, Conrad Huang and Tom Goddard for CHIMERA and For linking to MODBASE from their databases, we thank Torsten Schwede (Protein Model Portal  ... 
doi:10.1093/nar/gkt1144 pmid:24271400 pmcid:PMC3965011 fatcat:qjyw5cf25ndxpmlts7drmoc5ku

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

U. Pieper, B. M. Webb, D. T. Barkan, D. Schneidman-Duhovny, A. Schlessinger, H. Braberg, Z. Yang, E. C. Meng, E. F. Pettersen, C. C. Huang, R. S. Datta, P. Sampathkumar (+5 others)
2010 Nucleic Acids Research  
ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models.  ...  ModBase allows users to update comparative models on demand, and request modeling of additional sequences through an interface to the ModWeb modeling server  ...  Here, we describe the current state of the ModBase database of comparative protein structure models, the ModWeb comparative modeling web-server and several new associated resources: the SALIGN server for  ... 
doi:10.1093/nar/gkq1091 pmid:21097780 pmcid:PMC3013688 fatcat:kmqbpcx7sfek7jxgh4mmv2vley

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

U. Pieper, N. Eswar, B. M. Webb, D. Eramian, L. Kelly, D. T. Barkan, H. Carter, P. Mankoo, R. Karchin, M. A. Marti-Renom, F. P. Davis, A. Sali
2009 Nucleic Acids Research  
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  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkn791 pmid:18948282 pmcid:PMC2686492 fatcat:uy2vgrqqljfuhozumatnojgolu

ModBase: A database of comparative protein structure models

R. Sanchez
1999 Bioinformatics  
MODBASE is a database of evaluated and annotated comparative protein structure models. The database also includes fold assignments and alignments on which the models were based.  ...  Availability: MODBASE is accessible on the Web at http:// guitar.rockefeller.edu/ modbase. Models for yeast proteins are also accessible through links from the SACCH3D database at  ...  Steve A. Chervitz for making links from SGD to MODBASE and Paul de Bakker for help in implementing the WWW interface. RS is a Howard Hughes Medical Institute predoctoral fellow.  ... 
doi:10.1093/bioinformatics/15.12.1060 pmid:10745998 fatcat:mdrm7xnqy5di7ibbdbck56klnu

Tools for comparative protein structure modeling and analysis

N. Eswar
2003 Nucleic Acids Research  
of MODWEB for building comparative models based on distant known structures; MODBASE, a comprehensive database of annotated comparative models for all sequences detectably related to a known structure  ...  The following resources for comparative protein structure modeling and analysis are described (http://salilab.org): MODELLER, a program for comparative modeling by satisfaction of spatial restraints; MODWEB  ...  MODBASE MODBASE is a comprehensive relational database of annotated comparative protein structure models.  ... 
doi:10.1093/nar/gkg543 pmid:12824331 pmcid:PMC168950 fatcat:7h4x7vmc7rbh7nzath35dod2x4

Protein complex compositions predicted by structural similarity

F. P. Davis
2006 Nucleic Acids Research  
To generate candidate complexes, comparative models of individual proteins were built and combined together using complexes of known structure as templates.  ...  The statistical potential discriminated a benchmark set of 100 interface structures from a set of sequence-randomized negative examples with a false positive rate of 3% and a true positive rate of 97%.  ...  ACKNOWLEDGEMENTS We would like to thank members of the Sali laboratory for valuable comments and suggestions, in particular Maya Topf, Eswar Narayanan and Frank Alber.  ... 
doi:10.1093/nar/gkl353 pmid:16738133 pmcid:PMC1474056 fatcat:gnv7yrnjtrgv5krtn2b7aetcim

OnTheFly: a database ofDrosophila melanogastertranscription factors and their binding sites

Shula Shazman, Hunjoong Lee, Yakov Socol, Richard S. Mann, Barry Honig
2013 Nucleic Acids Research  
An important feature of the database is that all DNAbinding domains and their binding sites are fully annotated in a eukaryote using structural criteria and evolutionary homology.  ...  DNA shape parameters predicted for these sites are obtained from a high throughput server or from crystal structures of protein-DNA complexes where available.  ...  Homology models were found in Modbase for 1171 of the D. melanogaster TFs and stored in OnTheFly. Homology models in Modbase all have e-values < 10 À4 .  ... 
doi:10.1093/nar/gkt1165 pmid:24271386 pmcid:PMC3965123 fatcat:pk56picuxjdgflvrpvylyjkrha

High-Throughput Computational and Experimental Techniques in Structural Genomics

M. R. Chance
2004 Genome Research  
Comparative modeling of these structures has generated >40,000 structural models.  ...  The Consortium has established a pipeline for structural biology studies, automated modeling of ORF sequences using solved (template) structures, and a novel high-throughput approach (metallomics) to examining  ...  MODBASE (http://salilab.org/modbase) is a comprehensive database of annotated comparative protein structure models (Pieper et al.  ... 
doi:10.1101/gr.2537904 pmid:15489337 pmcid:PMC528931 fatcat:afjhww6uunhs5h6thcb6keefai

New developments in the InterPro database

N. J. Mulder, R. Apweiler, T. K. Attwood, A. Bairoch, A. Bateman, D. Binns, P. Bork, V. Buillard, L. Cerutti, R. Copley, E. Courcelle, U. Das (+33 others)
2007 Nucleic Acids Research  
The latest InterPro release (13.0) contains more than 13 000 entries, covering over 78% of all proteins in UniProtKB. The database is available for textand sequence-based searches via a webserver  ...  InterPro is an integrated resource for protein families, domains and functional sites, which integrates the following protein signature databases: PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs, PIRSF,  ...  A large proportion of HMMERbased calculations are performed on the IBMP690 Supercomputer at HLRN.  ... 
doi:10.1093/nar/gkl841 pmid:17202162 pmcid:PMC1899100 fatcat:ditkwsqd5zctdb5wgxs36xhmum

Annotation of virulence factors in schistosomes for the development of a SchistoVir database
English

S. Adebayo
2013 Journal of Computational Biology and Bioinformatics Research  
As a first step towards creating SchistoVir, a database of virulence protein factors in schistosomes, in this study, we curated, annotated and aligned sequences of twenty virulence factors identified from  ...  The annotations and characterization provided by this work and the development of a SchistoVir database will aid in further research of schistosome pathogenesis and control.  ...  MODBASE predicts a protein's 3D structure, when it is not available in its data bank (Pieper et al., 2011) . It is a tool for comparative protein structure modeling. 2.  ... 
doi:10.5897/jcbbr12.013 fatcat:b35yz2u4p5fpvf4paaargy6ora

Structure Based Annotation of Helicobacter pylori Strain 26695 Proteome

Swati Singh, Praveen Kumar Guttula, Lalitha Guruprasad, Narayanaswamy Srinivasan
2014 PLoS ONE  
Functional annotation of each protein was carried out based on structural fold and binding site based ligand association.  ...  Of the 1195 known structural folds present in the SCOP database, 411 (34% of all known folds) are observed in the whole H. pylori 26695 proteome, with greater inclination for domains belonging to a/b class  ...  Acknowledgments The authors thank Tummala Pavithra Devi for technical assistance in the initial stages of project. Author Contributions  ... 
doi:10.1371/journal.pone.0115020 pmid:25549250 pmcid:PMC4280198 fatcat:uk6lvqilzzfcnfquayjqpv73ta
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