FLAMEnGO 2.0: An enhanced fuzzy logic algorithm for structure-based assignment of methyl group resonances

Fa An Chao; Jonggul Kim; Youlin Xia; Michael Milligan; Nancy Rowe; Gianluigi Veglia

doi:10.1016/j.jmr.2014.04.012

FLAMEnGO 2.0: An enhanced fuzzy logic algorithm for structure-based assignment of methyl group resonances

Fa An Chao, Jonggul Kim, Youlin Xia, Michael Milligan, Nancy Rowe, Gianluigi Veglia

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

38 Scopus citations

Abstract

We present an enhanced version of the FLAMEnGO (Fuzzy Logic Assignment of Methyl Group) software, a structure-based method to assign methyl group resonances in large proteins. FLAMEnGO utilizes a fuzzy logic algorithm coupled with Monte Carlo sampling to obtain a probability-based assignment of the methyl group resonances. As an input, FLAMEnGO requires either the protein X-ray structure or an NMR structural ensemble including data such as methyl-methyl NOESY, paramagnetic relaxation enhancement (PRE), methine-methyl TOCSY data. Version 2.0 of this software (FLAMEnGO 2.0) has a user-friendly graphic interface and presents improved modules that enable the input of partial assignments and additional NMR restraints. We tested the performance of FLAMEnGO 2.0 on maltose binding protein (MBP) as well as the C-subunit of the cAMP-dependent protein kinase A (PKA-C). FLAMEnGO 2.0 can be used as a standalone method or to assist in the completion of partial resonance assignments and can be downloaded at www.chem.umn.edu/groups/veglia/forms/ flamengo2-form.html.

Original language	English (US)
Pages (from-to)	17-23
Number of pages	7
Journal	Journal of Magnetic Resonance
Volume	245
DOIs	https://doi.org/10.1016/j.jmr.2014.04.012
State	Published - Aug 2014

Bibliographical note

Funding Information:
This work was supported by the National Institute of Health ( GM 72701 and GM 100310 ). We would like to thank Unhyun Lee and Kaylee Steen for making and purifying mutant constructs of PKA-C. Moreover, we also appreciate the discussion with Dr. Kaustubh Mote, Dr. Alessandro Cembran, and Dr. Vitaly Vostrikov.

Keywords

Automatic assignment of methyl groups
FLAMEnGO 2.0
Methyl-TROSY
Sparse and ambiguous data

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10.1016/j.jmr.2014.04.012

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title = "FLAMEnGO 2.0: An enhanced fuzzy logic algorithm for structure-based assignment of methyl group resonances",

abstract = "We present an enhanced version of the FLAMEnGO (Fuzzy Logic Assignment of Methyl Group) software, a structure-based method to assign methyl group resonances in large proteins. FLAMEnGO utilizes a fuzzy logic algorithm coupled with Monte Carlo sampling to obtain a probability-based assignment of the methyl group resonances. As an input, FLAMEnGO requires either the protein X-ray structure or an NMR structural ensemble including data such as methyl-methyl NOESY, paramagnetic relaxation enhancement (PRE), methine-methyl TOCSY data. Version 2.0 of this software (FLAMEnGO 2.0) has a user-friendly graphic interface and presents improved modules that enable the input of partial assignments and additional NMR restraints. We tested the performance of FLAMEnGO 2.0 on maltose binding protein (MBP) as well as the C-subunit of the cAMP-dependent protein kinase A (PKA-C). FLAMEnGO 2.0 can be used as a standalone method or to assist in the completion of partial resonance assignments and can be downloaded at www.chem.umn.edu/groups/veglia/forms/ flamengo2-form.html.",

keywords = "Automatic assignment of methyl groups, FLAMEnGO 2.0, Methyl-TROSY, Sparse and ambiguous data",

author = "Chao, {Fa An} and Jonggul Kim and Youlin Xia and Michael Milligan and Nancy Rowe and Gianluigi Veglia",

note = "Funding Information: This work was supported by the National Institute of Health ( GM 72701 and GM 100310 ). We would like to thank Unhyun Lee and Kaylee Steen for making and purifying mutant constructs of PKA-C. Moreover, we also appreciate the discussion with Dr. Kaustubh Mote, Dr. Alessandro Cembran, and Dr. Vitaly Vostrikov. ",

year = "2014",

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doi = "10.1016/j.jmr.2014.04.012",

language = "English (US)",

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T1 - FLAMEnGO 2.0

T2 - An enhanced fuzzy logic algorithm for structure-based assignment of methyl group resonances

AU - Chao, Fa An

AU - Kim, Jonggul

AU - Xia, Youlin

AU - Milligan, Michael

AU - Rowe, Nancy

AU - Veglia, Gianluigi

N1 - Funding Information: This work was supported by the National Institute of Health ( GM 72701 and GM 100310 ). We would like to thank Unhyun Lee and Kaylee Steen for making and purifying mutant constructs of PKA-C. Moreover, we also appreciate the discussion with Dr. Kaustubh Mote, Dr. Alessandro Cembran, and Dr. Vitaly Vostrikov.

PY - 2014/8

Y1 - 2014/8

N2 - We present an enhanced version of the FLAMEnGO (Fuzzy Logic Assignment of Methyl Group) software, a structure-based method to assign methyl group resonances in large proteins. FLAMEnGO utilizes a fuzzy logic algorithm coupled with Monte Carlo sampling to obtain a probability-based assignment of the methyl group resonances. As an input, FLAMEnGO requires either the protein X-ray structure or an NMR structural ensemble including data such as methyl-methyl NOESY, paramagnetic relaxation enhancement (PRE), methine-methyl TOCSY data. Version 2.0 of this software (FLAMEnGO 2.0) has a user-friendly graphic interface and presents improved modules that enable the input of partial assignments and additional NMR restraints. We tested the performance of FLAMEnGO 2.0 on maltose binding protein (MBP) as well as the C-subunit of the cAMP-dependent protein kinase A (PKA-C). FLAMEnGO 2.0 can be used as a standalone method or to assist in the completion of partial resonance assignments and can be downloaded at www.chem.umn.edu/groups/veglia/forms/ flamengo2-form.html.

AB - We present an enhanced version of the FLAMEnGO (Fuzzy Logic Assignment of Methyl Group) software, a structure-based method to assign methyl group resonances in large proteins. FLAMEnGO utilizes a fuzzy logic algorithm coupled with Monte Carlo sampling to obtain a probability-based assignment of the methyl group resonances. As an input, FLAMEnGO requires either the protein X-ray structure or an NMR structural ensemble including data such as methyl-methyl NOESY, paramagnetic relaxation enhancement (PRE), methine-methyl TOCSY data. Version 2.0 of this software (FLAMEnGO 2.0) has a user-friendly graphic interface and presents improved modules that enable the input of partial assignments and additional NMR restraints. We tested the performance of FLAMEnGO 2.0 on maltose binding protein (MBP) as well as the C-subunit of the cAMP-dependent protein kinase A (PKA-C). FLAMEnGO 2.0 can be used as a standalone method or to assist in the completion of partial resonance assignments and can be downloaded at www.chem.umn.edu/groups/veglia/forms/ flamengo2-form.html.

KW - Automatic assignment of methyl groups

KW - FLAMEnGO 2.0

KW - Methyl-TROSY

KW - Sparse and ambiguous data

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ER -

FLAMEnGO 2.0: An enhanced fuzzy logic algorithm for structure-based assignment of methyl group resonances

Abstract

Bibliographical note

Keywords

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