(DP2)-P-2: database of disordered protein predictions

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

Research output: Contribution to journalArticle (Academic Journal)peer-review

314 Citations (Scopus)

Abstract

We present the Database of Disordered Protein Prediction ((DP2)-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. (DP2)-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.

Original languageEnglish
Pages (from-to)D508-D516
Number of pages9
JournalNucleic Acids Research
Volume41
Issue numberD1
DOIs
Publication statusPublished - Jan 2013

Keywords

  • INTRINSICALLY UNSTRUCTURED PROTEINS
  • SECONDARY STRUCTURE PREDICTION
  • NATIVELY UNFOLDED PROTEINS
  • SEQUENCE
  • REGIONS
  • CLASSIFICATION
  • DOMAINS
  • SERVER
  • CONSERVATION
  • ANNOTATIONS

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