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Bioinformatics Advance Access published online on April 21, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn132
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

OnD-CRF: predicting order and disorder in proteins using conditional random fields

Lixiao Wang and Uwe H. Sauer *

Umeå Centre for Molecular Pathogenesis, UCMP, and Centre for Chemical Biology, KBC, Umeå University, SE-901 87 Umeå, Sweden

*To whom correspondence should be addressed. Prof. Uwe H. Sauer, E-mail: Uwe.Sauer{at}ucmp.umu.se


  Abstract

Motivation: Order and Disorder prediction using Conditional Random Fields, OnD-CRF, is a new method for accurately predicting the transition between structured and mobile or disordered regions in proteins. OnD-CRF applies CRFs relying on features which are generated from the amino acids sequence and from secondary structure prediction. Benchmarking results based on CASP7 targets, and evaluation with respect to several CASP criteria, rank the OnD-CRF model highest among the fully automatic server group.

Availability: http://babel.ucmp.umu.se/ond-crf/

Contact: Uwe.Sauer{at}ucmp.umu.se

Associate Editor: Prof. Alfonso Valencia

Received on December 12, 2007; revised on April 6, 2008; accepted on April 8, 2008

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