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MODBASE, a database of annotated comparative protein structure models
2000
Nucleic Acids Research
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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
2002
Nucleic Acids Research
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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
2004
Nucleic Acids Research
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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
2006
Nucleic Acids Research
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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
2013
Nucleic Acids Research
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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
2010
Nucleic Acids Research
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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
2009
Nucleic Acids Research
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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
1999
Bioinformatics
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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
2003
Nucleic Acids Research
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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
2006
Nucleic Acids Research
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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
2013
Nucleic Acids Research
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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
2004
Genome Research
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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
2007
Nucleic Acids Research
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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
2013
Journal of Computational Biology and Bioinformatics Research
English
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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
2014
PLoS ONE
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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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