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Bioinformatics Advance Access originally published online on August 20, 2007
Bioinformatics 2007 23(18):2376-2384; doi:10.1093/bioinformatics/btm349
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© 2007 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.

Natively unstructured regions in proteins identified from contact predictions

Avner Schlessinger 1,2,*, Marco Punta 1,2 and Burkhard Rost 1,2

1Department of Biochemistry and Molecular Biophysics, Columbia University and 2Columbia University Center for Computational Biology and Bioinformatics (C2B2), NorthEast Structural Genomics Consortium (NESG), New York, NY, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Natively unstructured (also dubbed intrinsically disordered) regions in proteins lack a defined 3D structure under physiological conditions and often adopt regular structures under particular conditions. Proteins with such regions are overly abundant in eukaryotes, they may increase functional complexity of organisms and they usually evade structure determination in the unbound form. Low propensity for the formation of internal residue contacts has been previously used to predict natively unstructured regions.

Results: We combined PROFcon predictions for protein-specific contacts with a generic pairwise potential to predict unstructured regions. This novel method, Ucon, outperformed the best available methods in predicting proteins with long unstructured regions. Furthermore, Ucon correctly identified cases missed by other methods. By computing the difference between predictions based on specific contacts (approach introduced here) and those based on generic potentials (realized in other methods), we might identify unstructured regions that are involved in protein–protein binding. We discussed one example to illustrate this ambitious aim. Overall, Ucon added quality and an orthogonal aspect that may help in the experimental study of unstructured regions in network hubs.

Availability: http://www.predictprotein.org/submit_ucon.html

Contact: as2067{at}columbia.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Alex Bateman

Received on April 28, 2007; revised on June 26, 2007; accepted on June 27, 2007

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