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Bioinformatics Advance Access published online on November 29, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti797
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received June 26, 2005
Revised November 7, 2005
Accepted November 20, 2005

Applications note

Paircoil2: improved prediction of coiled coils from sequence

A. V. McDonnell 1, T. Jiang 2, A. E. Keating 3 *, and B. Berger 1

1 Mathematics Department, Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139
2 Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; Current address: Center for Computational and Systems Biology, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China
3 Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139

* To whom correspondence should be addressed.
A. E. Keating, E-mail: keating{at}mit.edu


  Abstract

Summary: We introduce Paircoil2, a new version of the Paircoil program, which uses pairwise residue probabilities to detect coiled-coil motifs in protein sequence data. Paircoil2 achieves 98% sensitivity and 97% specificity on known coiled coils in leave-family-out cross-validation. It also shows superior performance compared with published methods in tests on proteins of known structure.

Availability: Paircoil2 is freely available as a web application and for download at http://paircoil2.csail.mit.edu.

Supplementary Information: Available at the journal's web site and at the Paircoil2 web site.


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