Paircoil2: improved prediction of coiled coils from sequence

McDonnell, A. V.
Jiang, T.
Keating, A. E.
Berger, B.

¹Mathematics Department, Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, USA
²Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

Received on June 26, 2005; revised on November 7, 2005; accepted on November 20, 2005; Advance Access publication November 29, 2005

Associate Editor: Alfonso Valencia

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

Contact: [email protected]; [email protected]

Supplementary information: Available at Bioinformatics online and at the Paircoil website.

^*To whom correspondence should be addressed.

^†Present address: Center for Computational and Systems Biology, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China

Bioinformatics 22(3):p 356-358, February 1, 2006.

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.