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Bioinformatics Advance Access originally published online on June 9, 2005
Bioinformatics 2005 21(16):3369-3376; doi:10.1093/bioinformatics/bti534
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins

Zheng Rong Yang 1, Rebecca Thomson 2, Philip McNeil 3 and Robert M. Esnouf 2,*

1School of Engineering and Computer Science, Exeter University Exeter EX4 4QF, UK
2Division of Structural Biology and Oxford Protein Production Facility, University of Oxford Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN, UK
3European Bioinformatics Institute, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK

*To whom correspondence should be addressed.

Motivation: Recent studies have found many proteins containing regions that do not form well-defined three-dimensional structures in their native states. The study and detection of such disordered regions is important both for understanding protein function and for facilitating structural analysis since disordered regions may affect solubility and/or crystallizability.

Results: We have developed the regional order neural network (RONN) software as an application of our recently developed ‘bio-basis function neural network’ pattern recognition algorithm to the detection of natively disordered regions in proteins. The results of blind-testing a panel of nine disorder prediction tools (including RONN) against 80 protein sequences derived from the Protein Data Bank shows that, based on the probability excess measure, RONN performed the best.

Availability: RONN is available at http://www.strubi.ox.ac.uk/RONN. Requests for the RONN software and the database of disorder (XML format) can be directed to the corresponding author.

Contact: robert{at}strubi.ox.ac.uk

Supplementary information: Details of all predictions made during blind testing, also available at http://www.strubi.ox.ac.uk/RONN3_Supplementary.pdf

Received on July 9, 2004; revised on June 7, 2005; accepted on June 8, 2005

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