MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships.
Type
ArticleKAUST Grant Number
KUK-I1-012-43Date
2013-02-08Online Publication Date
2013-02-08Print Publication Date
2013-04-01Permanent link to this record
http://hdl.handle.net/10754/596803
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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.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.Publisher
Oxford University Press (OUP)Journal
BioinformaticsPubMed ID
23396123PubMed Central ID
PMC3605600ae974a485f413a2113503eed53cd6c53
10.1093/bioinformatics/btt062
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