title: RepeatsDB: a database of tandem repeat protein structures.
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.
authors: 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 and Institut de Biologie Computationnelle, 34293 Montpellier Cedex 5, France.
authors: Tomás
authors: T
authors: Di Domenico
authors: Emilio
authors: E
authors: Potenza
authors: Ian
authors: I
authors: Walsh
authors: R Gonzalo
authors: RG
authors: Parra
authors: Manuel
authors: M
authors: Giollo
authors: Giovanni
authors: G
authors: Minervini
authors: Damiano
authors: D
authors: Piovesan
authors: Awais
authors: A
authors: Ihsan
authors: Carlo
authors: C
authors: Ferrari
authors: Andrey V
authors: AV
authors: Kajava
authors: Silvio C E
authors: SC
authors: Tosatto
mesh_terms: D030562:Databases, Protein; D020407:Internet; D058977:Molecular Sequence Annotation; D011487:Protein Conformation; D020449:Repetitive Sequences, Amino Acid