RepeatsDB: A database of tandem repeat protein structures

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 the...

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Autores principales: 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.
Formato: JOUR
Materias:
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
Article
data analysis
Databases, Protein
Molecular Sequence Annotation
Protein Conformation
Repetitive Sequences, Amino Acid
Acceso en línea:http://hdl.handle.net/20.500.12110/paper_03051048_v42_nD1_pD352_DiDomenico
Aporte de:
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires
id todo:paper_03051048_v42_nD1_pD352_DiDomenico
record_format dspace
spelling todo:paper_03051048_v42_nD1_pD352_DiDomenico2023-10-03T15:21:32Z RepeatsDB: A database of tandem repeat protein structures 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. 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 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. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_03051048_v42_nD1_pD352_DiDomenico
institution Universidad de Buenos Aires
institution_str I-28
repository_str R-134
collection Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic 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
spellingShingle 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
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
topic_facet 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
description 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.
format JOUR
author 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.
author_facet 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.
author_sort Di Domenico, T.
title RepeatsDB: A database of tandem repeat protein structures
title_short RepeatsDB: A database of tandem repeat protein structures
title_full RepeatsDB: A database of tandem repeat protein structures
title_fullStr RepeatsDB: A database of tandem repeat protein structures
title_full_unstemmed RepeatsDB: A database of tandem repeat protein structures
title_sort repeatsdb: a database of tandem repeat protein structures
url http://hdl.handle.net/20.500.12110/paper_03051048_v42_nD1_pD352_DiDomenico
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AT potenzae repeatsdbadatabaseoftandemrepeatproteinstructures
AT walshi repeatsdbadatabaseoftandemrepeatproteinstructures
AT gonzaloparrar repeatsdbadatabaseoftandemrepeatproteinstructures
AT giollom repeatsdbadatabaseoftandemrepeatproteinstructures
AT minervinig repeatsdbadatabaseoftandemrepeatproteinstructures
AT piovesand repeatsdbadatabaseoftandemrepeatproteinstructures
AT ihsana repeatsdbadatabaseoftandemrepeatproteinstructures
AT ferraric repeatsdbadatabaseoftandemrepeatproteinstructures
AT kajavaav repeatsdbadatabaseoftandemrepeatproteinstructures
AT tosattosce repeatsdbadatabaseoftandemrepeatproteinstructures
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