MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships.

Handle URI:
http://hdl.handle.net/10754/596803
Title:
MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships.
Authors:
Kosinski, Jan; Barbato, Alessandro; Tramontano, Anna
Abstract:
SUMMARY: MODexplorer is an integrated tool aimed at exploring the sequence, structural and functional diversity in protein families useful in homology modeling and in analyzing protein families in general. It takes as input either the sequence or the structure of a protein and provides alignments with its homologs along with a variety of structural and functional annotations through an interactive interface. The annotations include sequence conservation, similarity scores, ligand-, DNA- and RNA-binding sites, secondary structure, disorder, crystallographic structure resolution and quality scores of models implied by the alignments to the homologs of known structure. MODexplorer can be used to analyze sequence and structural conservation among the structures of similar proteins, to find structures of homologs solved in different conformational state or with different ligands and to transfer functional annotations. Furthermore, if the structure of the query is not known, MODexplorer can be used to select the modeling templates taking all this information into account and to build a comparative model. AVAILABILITY AND IMPLEMENTATION: Freely available on the web at http://modorama.biocomputing.it/modexplorer. Website implemented in HTML and JavaScript with all major browsers supported. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Citation:
Kosinski J, Barbato A, Tramontano A (2013) MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships. Bioinformatics 29: 953–954. Available: http://dx.doi.org/10.1093/bioinformatics/btt062.
Publisher:
Oxford University Press (OUP)
Journal:
Bioinformatics
KAUST Grant Number:
KUK-I1-012-43
Issue Date:
8-Feb-2013
DOI:
10.1093/bioinformatics/btt062
PubMed ID:
23396123
PubMed Central ID:
PMC3605600
Type:
Article
ISSN:
1367-4803; 1460-2059
Sponsors:
KAUST Award No. KUK-I1-012-43 made by King Abdullah University of Science and Technology (KAUST), Fondazione Roma, FIRB Italbionet and RBIN06E9Z8_005, and European Molecular Biology Organization (EMBO) Long-Term Fellowship to J.K.
Appears in Collections:
Publications Acknowledging KAUST Support

Full metadata record

DC FieldValue Language
dc.contributor.authorKosinski, Janen
dc.contributor.authorBarbato, Alessandroen
dc.contributor.authorTramontano, Annaen
dc.date.accessioned2016-02-21T08:50:59Zen
dc.date.available2016-02-21T08:50:59Zen
dc.date.issued2013-02-08en
dc.identifier.citationKosinski J, Barbato A, Tramontano A (2013) MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships. Bioinformatics 29: 953–954. Available: http://dx.doi.org/10.1093/bioinformatics/btt062.en
dc.identifier.issn1367-4803en
dc.identifier.issn1460-2059en
dc.identifier.pmid23396123en
dc.identifier.doi10.1093/bioinformatics/btt062en
dc.identifier.urihttp://hdl.handle.net/10754/596803en
dc.description.abstractSUMMARY: MODexplorer is an integrated tool aimed at exploring the sequence, structural and functional diversity in protein families useful in homology modeling and in analyzing protein families in general. It takes as input either the sequence or the structure of a protein and provides alignments with its homologs along with a variety of structural and functional annotations through an interactive interface. The annotations include sequence conservation, similarity scores, ligand-, DNA- and RNA-binding sites, secondary structure, disorder, crystallographic structure resolution and quality scores of models implied by the alignments to the homologs of known structure. MODexplorer can be used to analyze sequence and structural conservation among the structures of similar proteins, to find structures of homologs solved in different conformational state or with different ligands and to transfer functional annotations. Furthermore, if the structure of the query is not known, MODexplorer can be used to select the modeling templates taking all this information into account and to build a comparative model. AVAILABILITY AND IMPLEMENTATION: Freely available on the web at http://modorama.biocomputing.it/modexplorer. Website implemented in HTML and JavaScript with all major browsers supported. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.en
dc.description.sponsorshipKAUST Award No. KUK-I1-012-43 made by King Abdullah University of Science and Technology (KAUST), Fondazione Roma, FIRB Italbionet and RBIN06E9Z8_005, and European Molecular Biology Organization (EMBO) Long-Term Fellowship to J.K.en
dc.publisherOxford University Press (OUP)en
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.rights.urihttp://creativecommons.org/licenses/by/3.0en
dc.subject.meshStructural Homology, Proteinen
dc.subject.meshSoftwareen
dc.titleMODexplorer: an integrated tool for exploring protein sequence, structure and function relationships.en
dc.typeArticleen
dc.identifier.journalBioinformaticsen
dc.identifier.pmcidPMC3605600en
dc.contributor.institutionDepartment of Physics, Sapienza University, 00185 Rome, Italy.en
kaust.grant.numberKUK-I1-012-43en
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