title: RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures.
abstract: RepeatsDB 2.0 (URL: http://repeatsdb.bio.unipd.it/) is an update of the database of annotated tandem repeat protein structures. Repeat proteins are a widespread class of non-globular proteins carrying heterogeneous functions involved in several diseases. Here we provide a new version of RepeatsDB with an improved classification schema including high quality annotations for ∼5400 protein structures. RepeatsDB 2.0 features information on start and end positions for the repeat regions and units for all entries. The extensive growth of repeat unit characterization was possible by applying the novel ReUPred annotation method over the entire Protein Data Bank, with data quality is guaranteed by an extensive manual validation for >60% of the entries. The updated web interface includes a new search engine for complex queries and a fully re-designed entry page for a better overview of structural data. It is now possible to compare unit positions, together with secondary structure, fold information and Pfam domains. Moreover, a new classification level has been introduced on top of the existing scheme as an independent layer for sequence similarity relationships at 40%, 60% and 90% identity.
authors.affiliation: Dept. of Biomedical Sciences, University of Padua, 35121 Padova, Italy.
authors.forename: Lisanna
authors.initials: L
authors.lastname: Paladin
authors.affiliation: Dept. of Biomedical Sciences, University of Padua, 35121 Padova, Italy.|Departamento de Ingeniería, Pontificia Universidad Católica del Perú, 32 Lima, Perú.
authors.forename: Layla
authors.initials: L
authors.lastname: Hirsh
authors.affiliation: Dept. of Biomedical Sciences, University of Padua, 35121 Padova, Italy.
authors.forename: Damiano
authors.initials: D
authors.lastname: Piovesan
authors.affiliation: Institute of Molecular Biology, Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany.
authors.forename: Miguel A
authors.initials: MA
authors.lastname: Andrade-Navarro
authors.affiliation: Centre de Recherches de Biochimie Macromoléculaire, CNRS, Université Montpellier, 34293 Montpellier, France.|Institut de Biologie Computationnelle (IBC), 34293 Montpellier, France.|Institute of Bioengineering, University ITMO, 197101 St. Petersburg, Russia.
authors.forename: Andrey V
authors.initials: AV
authors.lastname: Kajava
authors.affiliation: Dept. of Biomedical Sciences, University of Padua, 35121 Padova, Italy silvio.tosatto@unipd.it.|CNR Institute of Neuroscience, 35121 Padova, Italy.
authors.forename: Silvio C E
authors.identifier: 0000-0003-4525-7793
authors.initials: SC
authors.lastname: Tosatto
mesh_terms: D000818:Animals; D030562:Databases, Protein / Q000706:statistics & numerical data; D006801:Humans; D011506:Proteins / Q000145:classification; D020449:Repetitive Sequences, Amino Acid; D012984:Software; D013329:Structure-Activity Relationship
chemical_list: D011506:Proteins