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

被引：36

作者：

Chao, Fa-An ^{[1
]}

Kim, Jonggul ^{[2
]}

Xia, Youlin ^{[1
]}

Milligan, Michael ^{[3
]}

Rowe, Nancy ^{[3
]}

Veglia, Gianluigi ^{[1
,2
]}

机构：

[1] Univ Minnesota, Dept Biochem Mol Biol & Biophys, Minneapolis, MN 55445 USA

[2] Univ Minnesota, Dept Chem, Minneapolis, MN 55445 USA

[3] Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55445 USA

来源：

JOURNAL OF MAGNETIC RESONANCE | 2014年 / 245卷

关键词：

FLAMEnGO; 2.0; Automatic assignment of methyl groups; Methyl-TROSY; Sparse and ambiguous data; DEPENDENT PROTEIN-KINASE; MOLECULAR-WEIGHT PROTEINS; NMR; DYNAMICS; PROTEASOME; PROGRAM;

D O I：

10.1016/j.jmr.2014.04.012

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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. (C) 2014 Elsevier Inc. All rights reserved.

引用

页码：17 / 23

页数：7

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