D2P2: Database of disordered protein predictions

Matt E. Oates, Pedro Romero, Takashi Ishida, Mohamed Ghalwash, Marcin J. Mizianty, Bin Xue, Zsuzsanna Dosztányi, Vladimir N. Uversky, Zoran Obradovic, Lukasz Kurgan, A. Dunker, Julian Gough

Research output: Contribution to journalArticle

204 Citations (Scopus)

Abstract

We present the Database of Disordered Protein Prediction (D 2P2), 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. D2P2 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.

Original languageEnglish
JournalNucleic Acids Research
Volume41
Issue numberD1
DOIs
StatePublished - Jan 1 2013

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Protein Databases
Genome
Proteome
Proteins
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ASJC Scopus subject areas

  • Genetics

Cite this

Oates, M. E., Romero, P., Ishida, T., Ghalwash, M., Mizianty, M. J., Xue, B., ... Gough, J. (2013). D2P2: Database of disordered protein predictions. Nucleic Acids Research, 41(D1). https://doi.org/10.1093/nar/gks1226

D2P2 : Database of disordered protein predictions. / Oates, Matt E.; Romero, Pedro; Ishida, Takashi; Ghalwash, Mohamed; Mizianty, Marcin J.; Xue, Bin; Dosztányi, Zsuzsanna; Uversky, Vladimir N.; Obradovic, Zoran; Kurgan, Lukasz; Dunker, A.; Gough, Julian.

In: Nucleic Acids Research, Vol. 41, No. D1, 01.01.2013.

Research output: Contribution to journalArticle

Oates, ME, Romero, P, Ishida, T, Ghalwash, M, Mizianty, MJ, Xue, B, Dosztányi, Z, Uversky, VN, Obradovic, Z, Kurgan, L, Dunker, A & Gough, J 2013, 'D2P2: Database of disordered protein predictions', Nucleic Acids Research, vol. 41, no. D1. https://doi.org/10.1093/nar/gks1226
Oates ME, Romero P, Ishida T, Ghalwash M, Mizianty MJ, Xue B et al. D2P2: Database of disordered protein predictions. Nucleic Acids Research. 2013 Jan 1;41(D1). https://doi.org/10.1093/nar/gks1226
Oates, Matt E. ; Romero, Pedro ; Ishida, Takashi ; Ghalwash, Mohamed ; Mizianty, Marcin J. ; Xue, Bin ; Dosztányi, Zsuzsanna ; Uversky, Vladimir N. ; Obradovic, Zoran ; Kurgan, Lukasz ; Dunker, A. ; Gough, Julian. / D2P2 : Database of disordered protein predictions. In: Nucleic Acids Research. 2013 ; Vol. 41, No. D1.
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