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

J Magn Reson. 2014 Aug:245:17-23. doi: 10.1016/j.jmr.2014.04.012. Epub 2014 May 2.

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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms*
  • Cyclic AMP-Dependent Protein Kinases / chemistry*
  • Fuzzy Logic*
  • Maltose-Binding Proteins / chemistry*
  • Methane / analogs & derivatives*
  • Methane / analysis
  • Methane / chemistry
  • Monte Carlo Method
  • Nuclear Magnetic Resonance, Biomolecular / methods*
  • Pattern Recognition, Automated
  • Software*
  • User-Computer Interface

Substances

  • Maltose-Binding Proteins
  • methyl radical
  • Cyclic AMP-Dependent Protein Kinases
  • Methane