Literature DB >> 24915505

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

Fa-An Chao1, Jonggul Kim2, Youlin Xia1, Michael Milligan3, Nancy Rowe3, Gianluigi Veglia4.   

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.
Copyright © 2014 Elsevier Inc. All rights reserved.

Entities:  

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

Mesh：

Substances：

Year:  2014        PMID： 24915505      PMCID： PMC4161213          DOI： 10.1016/j.jmr.2014.04.012

Source DB:  PubMed          Journal:  J Magn Reson        ISSN： 1090-7807            Impact factor:   2.229


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