FLAMEnGO: A fuzzy logic approach for methyl group assignment using NOESY and paramagnetic relaxation enhancement data

Fa An Chao; Lei Shi; Larry R. Masterson; Gianluigi Veglia

doi:10.1016/j.jmr.2011.10.008

FLAMEnGO: A fuzzy logic approach for methyl group assignment using NOESY and paramagnetic relaxation enhancement data

Fa An Chao, Lei Shi, Larry R. Masterson, Gianluigi Veglia

Chemical and Structural Biology (TMED)

Research output: Contribution to journal › Article › peer-review

21 Scopus citations

Abstract

Building on a recent method by Matthews and co-workers [1], we developed a new and efficient algorithm to assign methyl resonances from sparse and ambiguous NMR data. The new algorithm (FLAMEnGO: Fuzzy Logic Assignment of MEthyl GrOups) uses Monte Carlo sampling in conjunction with fuzzy logic to obtain the assignment of methyl resonances at high fidelity. Furthermore, we demonstrate that the inclusion of paramagnetic relaxation enhancement (PRE) data in the assignment strategy increases the percentage of correct assignments with sparse NOE data. Using synthetic tests and experimental data we show that this new approach provides up to ∼80% correct assignments with only 30% of methyl-methyl NOE data. In the experimental case of ubiquitin, PRE data from two spin labeled sites improve the percentage of assigned methyl groups up to ∼91%. This new strategy promises to further expand methyl group NMR spectroscopy to very large macromolecular systems.

Original language	English (US)
Pages (from-to)	103-110
Number of pages	8
Journal	Journal of Magnetic Resonance
Volume	214
DOIs	https://doi.org/10.1016/j.jmr.2011.10.008
State	Published - Jan 2012

Bibliographical note

Funding Information:
This work was supported by the National Institute of Health (GM072701 to G.V. and T32DE007288 to L.R.M.). We also would like to thank Dr. Marco Tonelli at NMRFAM for assistance with the NMR spectroscopy. The scripts and instructions for FLAMEnGO are available at www.chem.umn.edu/groups/veglia under “downloads”.

Keywords

Automated assignment
Fuzzy logic
Methyl group assignments
Methyl-TROSY
Monte Carlo
Sparse NMR data

Access

10.1016/j.jmr.2011.10.008

OpenUrl availability

Full text

Cite this

@article{01ea3305b01f42a190ce4cebf50c201e,

title = "FLAMEnGO: A fuzzy logic approach for methyl group assignment using NOESY and paramagnetic relaxation enhancement data",

abstract = "Building on a recent method by Matthews and co-workers [1], we developed a new and efficient algorithm to assign methyl resonances from sparse and ambiguous NMR data. The new algorithm (FLAMEnGO: Fuzzy Logic Assignment of MEthyl GrOups) uses Monte Carlo sampling in conjunction with fuzzy logic to obtain the assignment of methyl resonances at high fidelity. Furthermore, we demonstrate that the inclusion of paramagnetic relaxation enhancement (PRE) data in the assignment strategy increases the percentage of correct assignments with sparse NOE data. Using synthetic tests and experimental data we show that this new approach provides up to ∼80% correct assignments with only 30% of methyl-methyl NOE data. In the experimental case of ubiquitin, PRE data from two spin labeled sites improve the percentage of assigned methyl groups up to ∼91%. This new strategy promises to further expand methyl group NMR spectroscopy to very large macromolecular systems.",

keywords = "Automated assignment, Fuzzy logic, Methyl group assignments, Methyl-TROSY, Monte Carlo, Sparse NMR data",

author = "Chao, {Fa An} and Lei Shi and Masterson, {Larry R.} and Gianluigi Veglia",

note = "Funding Information: This work was supported by the National Institute of Health (GM072701 to G.V. and T32DE007288 to L.R.M.). We also would like to thank Dr. Marco Tonelli at NMRFAM for assistance with the NMR spectroscopy. The scripts and instructions for FLAMEnGO are available at www.chem.umn.edu/groups/veglia under “downloads”. ",

year = "2012",

month = jan,

doi = "10.1016/j.jmr.2011.10.008",

language = "English (US)",

volume = "214",

pages = "103--110",

journal = "Journal of Magnetic Resonance",

issn = "1090-7807",

publisher = "Academic Press Inc.",

}

TY - JOUR

T1 - FLAMEnGO

T2 - A fuzzy logic approach for methyl group assignment using NOESY and paramagnetic relaxation enhancement data

AU - Chao, Fa An

AU - Shi, Lei

AU - Masterson, Larry R.

AU - Veglia, Gianluigi

N1 - Funding Information: This work was supported by the National Institute of Health (GM072701 to G.V. and T32DE007288 to L.R.M.). We also would like to thank Dr. Marco Tonelli at NMRFAM for assistance with the NMR spectroscopy. The scripts and instructions for FLAMEnGO are available at www.chem.umn.edu/groups/veglia under “downloads”.

PY - 2012/1

Y1 - 2012/1

N2 - Building on a recent method by Matthews and co-workers [1], we developed a new and efficient algorithm to assign methyl resonances from sparse and ambiguous NMR data. The new algorithm (FLAMEnGO: Fuzzy Logic Assignment of MEthyl GrOups) uses Monte Carlo sampling in conjunction with fuzzy logic to obtain the assignment of methyl resonances at high fidelity. Furthermore, we demonstrate that the inclusion of paramagnetic relaxation enhancement (PRE) data in the assignment strategy increases the percentage of correct assignments with sparse NOE data. Using synthetic tests and experimental data we show that this new approach provides up to ∼80% correct assignments with only 30% of methyl-methyl NOE data. In the experimental case of ubiquitin, PRE data from two spin labeled sites improve the percentage of assigned methyl groups up to ∼91%. This new strategy promises to further expand methyl group NMR spectroscopy to very large macromolecular systems.

AB - Building on a recent method by Matthews and co-workers [1], we developed a new and efficient algorithm to assign methyl resonances from sparse and ambiguous NMR data. The new algorithm (FLAMEnGO: Fuzzy Logic Assignment of MEthyl GrOups) uses Monte Carlo sampling in conjunction with fuzzy logic to obtain the assignment of methyl resonances at high fidelity. Furthermore, we demonstrate that the inclusion of paramagnetic relaxation enhancement (PRE) data in the assignment strategy increases the percentage of correct assignments with sparse NOE data. Using synthetic tests and experimental data we show that this new approach provides up to ∼80% correct assignments with only 30% of methyl-methyl NOE data. In the experimental case of ubiquitin, PRE data from two spin labeled sites improve the percentage of assigned methyl groups up to ∼91%. This new strategy promises to further expand methyl group NMR spectroscopy to very large macromolecular systems.

KW - Automated assignment

KW - Fuzzy logic

KW - Methyl group assignments

KW - Methyl-TROSY

KW - Monte Carlo

KW - Sparse NMR data

UR - http://www.scopus.com/inward/record.url?scp=84855677622&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84855677622&partnerID=8YFLogxK

U2 - 10.1016/j.jmr.2011.10.008

DO - 10.1016/j.jmr.2011.10.008

M3 - Article

C2 - 22134225

AN - SCOPUS:84855677622

SN - 1090-7807

VL - 214

SP - 103

EP - 110

JO - Journal of Magnetic Resonance

JF - Journal of Magnetic Resonance

ER -

FLAMEnGO: A fuzzy logic approach for methyl group assignment using NOESY and paramagnetic relaxation enhancement data

Abstract

Bibliographical note

Keywords

Access

OpenUrl availability

Other files and links

Fingerprint

Cite this