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Bioinformatics 2009 25(12):i268-i275; doi:10.1093/bioinformatics/btp225
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© 2009 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.

PICKY: a novel SVD-based NMR spectra peak picking method

Babak Alipanahi 1,{dagger}, Xin Gao 1,{dagger}, Emre Karakoc 1,{dagger}, Logan Donaldson 2 and Ming Li 1,*

1David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, ON, Canada N2L 3G1 and 2Department of Biology, York University, Toronto, ON, Canada M3J 1P3

*To whom correspondence should be addressed.


  Abstract

Motivation: Picking peaks from experimental NMR spectra is a key unsolved problem for automated NMR protein structure determination. Such a process is a prerequisite for resonance assignment, nuclear overhauser enhancement (NOE) distance restraint assignment, and structure calculation tasks. Manual or semi-automatic peak picking, which is currently the prominent way used in NMR labs, is tedious, time consuming and costly.

Results: We introduce new ideas, including noise-level estimation, component forming and sub-division, singular value decomposition (SVD)-based peak picking and peak pruning and refinement. PICKY is developed as an automated peak picking method. Different from the previous research on peak picking, we provide a systematic study of the proposed method. PICKY is tested on 32 real 2D and 3D spectra of eight target proteins, and achieves an average of 88% recall and 74% precision. PICKY is efficient. It takes PICKY on average 15.7 s to process an NMR spectrum. More important than these numbers, PICKY actually works in practice. We feed peak lists generated by PICKY to IPASS for resonance assignment, feed IPASS assignment to SPARTA for fragments generation, and feed SPARTA fragments to FALCON for structure calculation. This results in high-resolution structures of several proteins, for example, TM1112, at 1.25 Å.

Availability: PICKY is available upon request. The peak lists of PICKY can be easily loaded by SPARKY to enable a better interactive strategy for rapid peak picking.

Contact: mli{at}uwaterloo.ca

{dagger}The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors.


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