TY - JOUR
T1 - PICKY
T2 - A novel SVD-based NMR spectra peak picking method
AU - Alipanahi, Babak
AU - Gao, Xin
AU - Karakoc, Emre
AU - Donaldson, Logan
AU - Li, Ming
N1 - Funding Information:
Funding: NSERC (Grant OGP0046506, 863 Grant 2008AA02Z313) from China’s Ministry of Science and Technology; Canada Research Chair program; MITACS, an NSERC Collaborative Grant; SHARCNET; Cheriton Scholarship.
PY - 2009
Y1 - 2009
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=66349110095&partnerID=8YFLogxK
U2 - 10.1093/bioinformatics/btp225
DO - 10.1093/bioinformatics/btp225
M3 - Article
C2 - 19477998
AN - SCOPUS:66349110095
SN - 1367-4803
VL - 25
SP - i268-i275
JO - Bioinformatics
JF - Bioinformatics
IS - 12
ER -