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RepeatsDB specifications

Information


Unique identifier OMICS_11564
Name RepeatsDB
Restrictions to use None
Community driven No
Data access Browse, Application programming interface
User data submission Not allowed
Version 2.0
Maintained Yes

Documentation


Maintainer


  • person_outline Silvio Tosatto

Publications for RepeatsDB

RepeatsDB citations

 (5)
library_books

Evolution of Protein Domain Repeats in Metazoa

2016
Mol Biol Evol
PMCID: 5100051
PMID: 27671125
DOI: 10.1093/molbev/msw194

[…] omain repeats are composed of units that fold cooperatively into either long “elongated” structures, circular “closed” structures, or a collection of units that can fold independently (see top). The RepeatsDB project () provides annotations of structures from PDB entries () according to this schema. We used hmmbuild and hmmscan from the HMMER3 package () to first construct HMMs based on MSAs of e […]

library_books

Expansion and Function of Repeat Domain Proteins During Stress and Development in Plants

2016
Front Plant Sci
PMCID: 4707873
PMID: 26793205
DOI: 10.3389/fpls.2015.01218

[…] repeats of variable length. The utilization of both XSTREAM and T-REKS is not limited only for amino acid sequences but these can also be applied to the DNA sequences ().Some other databases such as RepeatsDB, provides a systemic annotation and classification of repeats based on their structure (). RepeatsDB is a collection of predicted repeat units derived from Protein Data Bank (), which were s […]

library_books

Structural and Energetic Characterization of the Ankyrin Repeat Protein Family

2015
PLoS Comput Biol
PMCID: 4687027
PMID: 26691182
DOI: 10.1371/journal.pcbi.1004659

[…] ation and sequence coverage of ANKs at sequence databases such as Pfam, Uniprot and definitively would be useful in order to perform consistent high-quality annotation on structural databases such as RepeatsDB [] in which all repeat-containing proteins are being deposited and characterized.We have shown that the N-terminal, internal and C-terminal repeats are different in their sequence and energe […]

library_books

Tandem Repeats in Proteins: Prediction Algorithms and Biological Role

2015
Front Bioeng Biotechnol
PMCID: 4585158
PMID: 26442257
DOI: 10.3389/fbioe.2015.00143

[…] rent species; moreover, it includes 85 completely sequenced eukaryotic proteomes from the RefSeq collection. The latest datasets used in ProRepeat are UniProtKB Release May 2011 and RefSeq Release 40.RepeatsDB (Di Domenico et al., ) is a database of annotated tandem repeat protein structures that uses both a state of the art detection method (RAPHAEL) and manual curation to survey the protein stru […]

library_books

The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection

2013
Nucleic Acids Res
PMCID: 3965027
PMID: 24316579
DOI: 10.1093/nar/gkt1282

[…] updates on UniProt and KEGG, as well as updates of such popular databases as Pfam, eggNOG, ELM, FireDB, SEED, SIMAP and Transporter protein Classification DataBase (TCDB). Two new databases, HRaP and RepeatsDB, collect information on protein repeats, the former at the sequence level (runs of the same amino acid residue) and the latter at the structural level (,).As in previous years, this Database […]

Citations

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RepeatsDB institution(s)
Department of Biomedical Sciences, University of Padua, Padova, Italy; Departamento de Ingeniería, Pontificia Universidad Católica del Perú, Lima, Perú; Institute of Molecular Biology, Faculty of Biology, Johannes Gutenberg University of Mainz, Mainz, Germany; Centre de Recherches de Biochimie Macromoléculaire, CNRS, Université Montpellier, Montpellier, France; Institut de Biologie Computationnelle (IBC), Montpellier, France; Institute of Bioengineering, University ITMO, St. Petersburg, Russia; CNR Institute of Neuroscience, Padova, Italy
RepeatsDB funding source(s)
COST Action BM1405 NGP-net

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