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PMID: 23203878 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

D²P²: database of disordered protein predictions.

Nucleic acids research ·Vol. 41 ·No. Database issue ·2013-01-00 ·Pages D508-16

Oates ME, Romero P, Ishida T, Ghalwash M, Mizianty MJ, Xue B, Dosztányi Z, Uversky VN, Obradovic Z, Kurgan L, Dunker AK, Gough J

Abstract

We present the Database of Disordered Protein Prediction (D(2)P(2)), available at http://d2p2.pro (including website source code). A battery of disorder predictors and their variants, VL-XT, VSL2b, PrDOS, PV2, Espritz and IUPred, were run on all protein sequences from 1765 complete proteomes (to be updated as more genomes are completed). Integrated with these results are all of the predicted (mostly structured) SCOP domains using the SUPERFAMILY predictor. These disorder/structure annotations together enable comparison of the disorder predictors with each other and examination of the overlap between disordered predictions and SCOP domains on a large scale. D(2)P(2) will increase our understanding of the interplay between disorder and structure, the genomic distribution of disorder, and its evolutionary history. The parsed data are made available in a unified format for download as flat files or SQL tables either by genome, by predictor, or for the complete set. An interactive website provides a graphical view of each protein annotated with the SCOP domains and disordered regions from all predictors overlaid (or shown as a consensus). There are statistics and tools for browsing and comparing genomes and their disorder within the context of their position on the tree of life.

MeSH Terms
Databases, Protein Genome Internet Protein Conformation Protein Structure, Tertiary Proteins/chemistry,genetics Sequence Analysis, Protein
Chemicals
Proteins
Authors & Affiliations
12 authors, click to expand affiliations / ORCID
Oates Matt E
Department of Computer Science, University of Bristol, Bristol BS8 1UB, UK. Matt.Oates@bristol.ac.uk
Romero Pedro
Ishida Takashi
Ghalwash Mohamed
Mizianty Marcin J
Xue Bin
Dosztányi Zsuzsanna
Uversky Vladimir N
Obradovic Zoran
Kurgan Lukasz
Dunker A Keith
Gough Julian
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gks1226
Email
matt.oates@bristol.ac.uk
Published
2013-01-00
Epub
2012-00-29
Pages
D508-16
Language
English
Region
England
NLM ID
0411011
PMCID
PMC3531159
Subset
IM
Grants
Biotechnology and Biological Sciences Research Council · BB/G022771/1 · United Kingdom
External Links
PubMed source DOI: 10.1093/nar/gks1226 PMC Full Text View journal details
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