POODLE-I

Disordered region prediction by integrating POODLE series and structural information predictors based on a workflow approach

Shuichi Hirose, Kana Shimizu, Tamotsu Noguchi

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

Under physiological conditions, many proteins that include a region lacking well-defined three-dimensional structures have been identified, especially in eukaryotes. These regions often play an important biological cellular role, although they cannot form a stable structure. Therefore, they are biologically remarkable phenomena. From an industrial perspective, they can provide useful information for determining three-dimensional structures or designing drugs. For these reasons, disordered regions have attracted a great deal of attention in recent years. Their accurate prediction is therefore anticipated to provide annotations that are useful for wide range of applications. POODLE-I (where "I" stands for integration) is a web-based disordered region prediction system. POODLE-I integrates prediction results obtained from three kinds of disordered region predictors (POODLEs) developed from the viewpoint that the characteristics of disordered regions change according to their length. Furthermore, POODLE-I combines that information with predicted structural information by application of a workflow approach. When compared with server teams that showed best performance in CASP8, POODLE-I ranked among the top and exhibited the highest performance in predicting unfolded proteins. POODLE-I is an efficient tool for detecting disordered regions in proteins solely from the amino acid sequence. The application is freely available at http://mbs.cbrc.jp/ poodle/poodle-i.html.

Original languageEnglish
Pages (from-to)185-191
Number of pages7
JournalIn Silico Biology
Volume10
Issue number3-4
DOIs
Publication statusPublished - 2010
Externally publishedYes

Fingerprint

Workflow
Work Flow
Predictors
Proteins
Protein Unfolding
Series
Prediction
Eukaryota
Amino Acid Sequence
Amino acids
Protein
Servers
Pharmaceutical Preparations
Three-dimensional
Web-based
Annotation
Well-defined
Drugs
Server
High Performance

Keywords

  • accessible surface area
  • CASP
  • coiled coil
  • Disordered region
  • fold recognition
  • secondary structure
  • unfolded protein
  • workflow

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Computational Mathematics
  • Computational Theory and Mathematics

Cite this

POODLE-I : Disordered region prediction by integrating POODLE series and structural information predictors based on a workflow approach. / Hirose, Shuichi; Shimizu, Kana; Noguchi, Tamotsu.

In: In Silico Biology, Vol. 10, No. 3-4, 2010, p. 185-191.

Research output: Contribution to journalArticle

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