Artículo

Di Domenico, T.; Potenza, E.; Walsh, I.; Gonzalo Parra, R.; Giollo, M.; Minervini, G.; Piovesan, D.; Ihsan, A.; Ferrari, C.; Kajava, A.V.; Tosatto, S.C.E. "RepeatsDB: A database of tandem repeat protein structures" (2014) Nucleic Acids Research. 42(D1):D352-D357
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Abstract:

RepeatsDB (http://repeatsdb.bio.unipd.it/) is a database of annotated tandem repeat protein structures. Tandem repeats pose a difficult problem for the analysis of protein structures, as the underlying sequence can be highly degenerate. Several repeat types haven been studied over the years, but their annotation was done in a case-by-case basis, thus making large-scale analysis difficult. We developed RepeatsDB to fill this gap. Using state-of-the-art repeat detection methods and manual curation, we systematically annotated the Protein Data Bank, predicting 10 745 repeat structures. In all, 2797 structures were classified according to a recently proposed classification schema, which was expanded to accommodate new findings. In addition, detailed annotations were performed in a subset of 321 proteins. These annotations feature information on start and end positions for the repeat regions and units. RepeatsDB is an ongoing effort to systematically classify and annotate structural protein repeats in a consistent way. It provides users with the possibility to access and download high-quality datasets either interactively or programmatically through web services. © 2013 The Author(s). Published by Oxford University Press.

Registro:

Documento: Artículo
Título:RepeatsDB: A database of tandem repeat protein structures
Autor:Di Domenico, T.; Potenza, E.; Walsh, I.; Gonzalo Parra, R.; Giollo, M.; Minervini, G.; Piovesan, D.; Ihsan, A.; Ferrari, C.; Kajava, A.V.; Tosatto, S.C.E.
Filiación:Department of Biomedical Sciences, University of Padua, 35131 Padova, Italy
Department of Biological Chemistry, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
Department of Information Engineering, University of Padua, 35121 Padova, Italy
Department of Biosciences, COMSATS Institute of Information Technology, Sahiwal, Pakistan
Centre de Recherches de Biochimie Macromoléculaire, CNRS, 34293 Montpellier Cedex 5, France
Institut de Biologie Computationnelle, 34293 Montpellier Cedex 5, France
Palabras clave:article; information processing; information retrieval; priority journal; protein database; protein secondary structure; protein structure; structure analysis; tandem repeat; web browser; amino acid sequence; Internet; molecular genetics; protein conformation; access to information; amino acid sequence; Article; data analysis; Databases, Protein; Internet; Molecular Sequence Annotation; Protein Conformation; Repetitive Sequences, Amino Acid
Año:2014
Volumen:42
Número:D1
Página de inicio:D352
Página de fin:D357
DOI: http://dx.doi.org/10.1093/nar/gkt1175
Título revista:Nucleic Acids Research
Título revista abreviado:Nucleic Acids Res.
ISSN:03051048
CODEN:NARHA
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_03051048_v42_nD1_pD352_DiDomenico

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Citas:

---------- APA ----------
Di Domenico, T., Potenza, E., Walsh, I., Gonzalo Parra, R., Giollo, M., Minervini, G., Piovesan, D.,..., Tosatto, S.C.E. (2014) . RepeatsDB: A database of tandem repeat protein structures. Nucleic Acids Research, 42(D1), D352-D357.
http://dx.doi.org/10.1093/nar/gkt1175
---------- CHICAGO ----------
Di Domenico, T., Potenza, E., Walsh, I., Gonzalo Parra, R., Giollo, M., Minervini, G., et al. "RepeatsDB: A database of tandem repeat protein structures" . Nucleic Acids Research 42, no. D1 (2014) : D352-D357.
http://dx.doi.org/10.1093/nar/gkt1175
---------- MLA ----------
Di Domenico, T., Potenza, E., Walsh, I., Gonzalo Parra, R., Giollo, M., Minervini, G., et al. "RepeatsDB: A database of tandem repeat protein structures" . Nucleic Acids Research, vol. 42, no. D1, 2014, pp. D352-D357.
http://dx.doi.org/10.1093/nar/gkt1175
---------- VANCOUVER ----------
Di Domenico, T., Potenza, E., Walsh, I., Gonzalo Parra, R., Giollo, M., Minervini, G., et al. RepeatsDB: A database of tandem repeat protein structures. Nucleic Acids Res. 2014;42(D1):D352-D357.
http://dx.doi.org/10.1093/nar/gkt1175