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.
authors.affiliation: Department of Biochemistry, Molecular Biology, & Biophysics, University of Minnesota, Minneapolis, MN 55445, United States.
authors.forename: Fa-An
authors.initials: FA
authors.lastname: Chao
authors.affiliation: Department of Chemistry, University of Minnesota, Minneapolis, MN 55445, United States.
authors.forename: Jonggul
authors.initials: J
authors.lastname: Kim
authors.affiliation: Department of Biochemistry, Molecular Biology, & Biophysics, University of Minnesota, Minneapolis, MN 55445, United States.
authors.forename: Youlin
authors.initials: Y
authors.lastname: Xia
authors.affiliation: Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55445, United States.
authors.forename: Michael
authors.initials: M
authors.lastname: Milligan
authors.affiliation: Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55445, United States.
authors.forename: Nancy
authors.initials: N
authors.lastname: Rowe
authors.affiliation: Department of Biochemistry, Molecular Biology, & Biophysics, University of Minnesota, Minneapolis, MN 55445, United States; Department of Chemistry, University of Minnesota, Minneapolis, MN 55445, United States. Electronic address: vegli001@umn.edu.
authors.forename: Gianluigi
authors.initials: G
authors.lastname: Veglia
mesh_terms: D000465:Algorithms; D017868:Cyclic AMP-Dependent Protein Kinases / Q000737:chemistry*; D017143:Fuzzy Logic; D058619:Maltose-Binding Proteins / Q000737:chemistry*; D008697:Methane / Q000031:analogs & derivatives* / Q000032:analysis / Q000737:chemistry; D009010:Monte Carlo Method; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D010363:Pattern Recognition, Automated; D012984:Software; D014584:User-Computer Interface
chemical_list: D058619:Maltose-Binding Proteins; C051224:methyl radical; D017868:Cyclic AMP-Dependent Protein Kinases; D008697:Methane
keywords: Automatic assignment of methyl groups; FLAMEnGO 2.0; Methyl-TROSY; Sparse and ambiguous data