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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. ...
Our other resources integrated with MODBASE include comprehensive databases of multiple protein structure alignments (DBAli, http://salilab.org/dbali), structurally defined ligand binding sites and structurally ...
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 currently contains 5 152 695 reliable models for domains in 1 593 209 unique protein sequences; only models based on statistically significant alignments and/or models assessed to have the correct ...
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
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
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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
New developments in the InterPro database
2007
Nucleic Acids Research
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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, ...
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 ...
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
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
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. ...
TFs predicted in the Drosophila melanogaster genome are annotated and classified and their structures, obtained via experiment or homology models, are provided. ...
Overall annotations of a protein (GO term, EC class) and annotations associated with individual residues (UniProt sequence features, ligand interactions) can be displayed and used to filter structural ...
doi:10.1093/nar/gkt1165
pmid:24271386
pmcid:PMC3965123
fatcat:pk56picuxjdgflvrpvylyjkrha
Structural Annotation of Mycobacterium tuberculosis Proteome
2011
PLoS ONE
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Functional annotation of each protein was based on fold-based functional assignments and a novel binding site based ligand association. ...
Structural models were obtained and validated for ,2877 ORFs, covering ,70% of the genome. ...
Acknowledgments This work forms a part of the Connect2Decode project (http://c2d.osdd. net/) for 'Re-annotation of Mycobacterium tuberculosis', an initiative of the Open Source Drug Discovery project. ...
doi:10.1371/journal.pone.0027044
pmid:22073123
pmcid:PMC3205055
fatcat:exqhqpoj2vdk3ge3th7qbqsj7m
Structural Annotation of the Mycobacterium tuberculosis Proteome
2014
Microbiology spectrum
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Functional annotation of each protein was based on fold-based functional assignments and a novel binding site based ligand association. ...
Structural models were obtained and validated for ,2877 ORFs, covering ,70% of the genome. ...
Acknowledgments This work forms a part of the Connect2Decode project (http://c2d.osdd. net/) for 'Re-annotation of Mycobacterium tuberculosis', an initiative of the Open Source Drug Discovery project. ...
doi:10.1128/microbiolspec.mgm2-0027-2013
pmid:26105824
fatcat:dcup7tpzmjc6xgomusgbietpvy
Bioinformatic Tools for Identifying Disease Gene and SNP Candidates
[chapter]
2010
Msphere
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As databases of genome data continue to grow, our understanding of the functional elements of the genome grows as well. ...
In this protocol manuscript, methods for understanding the molecular functions of single nucleotide polymorphisms (SNPs) and mutations are reviewed and described. ...
LS-SNP stands out as a useful and unique resource because it provides annotations of nsSNPs that have been mapped to homology models from the MODBASE (http://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi ...
doi:10.1007/978-1-60327-367-1_17
pmid:20238089
pmcid:PMC3957484
fatcat:z3svbfpslbajrbioo2qrjwwkei
Discovery-2: an interactive resource for the rational selection and comparison of putative drug target proteins in malaria
2013
Malaria Journal
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advanced filtering and selection of proteins based on a relevant range of molecular characteristics. ...
Discovery-2 is an update of the original Discovery in silico resource for the rational selection of putative drug target proteins, enabling researchers to obtain information for a protein which may be ...
Acknowledgements We thank John Overington and the ChEMBL group for hosting PM and MS for a research visit. We are grateful to ChemAxon for the FreeWeb license. ...
doi:10.1186/1475-2875-12-116
pmid:23537208
pmcid:PMC3637051
fatcat:tjpfomfagfc2ndzadfi2wlgcse
Discovery: an interactive resource for the rational selection and comparison of putative drug target proteins in malaria
2009
Malaria Journal
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2013; you can also visit the original URL.
The file type is application/pdf.
advanced filtering and selection of proteins based on a relevant range of molecular characteristics. ...
Discovery-2 is an update of the original Discovery in silico resource for the rational selection of putative drug target proteins, enabling researchers to obtain information for a protein which may be ...
Acknowledgements We thank John Overington and the ChEMBL group for hosting PM and MS for a research visit. We are grateful to ChemAxon for the FreeWeb license. ...
doi:10.1186/1475-2875-8-178
pmid:19642978
pmcid:PMC2724543
fatcat:yjm6x3ilengkjkufwjngxe3sbq
InterPro: the integrative protein signature database
2009
Nucleic Acids Research
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Additionally, if a protein has a solved 3D structure in PDB or a structure modelled in either the MODBASE (22) or SWISS-MODEL (23) databases, this information is shown together with the member databases ...
Each unique protein sequence is stored only once in A new file (feature.xml) has been created which contains non-signature match data from the structural databases (PDB, MODBASE and SWISS-MODEL) for UniProtKB ...
Conflict of interest statement. None declared. ...
doi:10.1093/nar/gkn785
pmid:18940856
pmcid:PMC2686546
fatcat:6ehhtr3amzazll5wha5itvjzba
The SWISS-MODEL Repository and associated resources
2009
Nucleic Acids Research
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SWISS-MODEL Repository (http://swissmodel. expasy.org/repository/) is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline. ...
facilitates the navigation between protein sequence and structure resources. ...
ACKNOWLEDGEMENTS We are grateful to Rainer Po¨hlmann, [BC] 2 & Biozentrum University of Basel, for professional systems support, Pascal Benkert for fruitful discussions on model quality assessment and ...
doi:10.1093/nar/gkn750
pmid:18931379
pmcid:PMC2686475
fatcat:tzaquxsk3vffzdprb7h5efkasq
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