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 journalArticlepeer-review

29 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 languageEnglish (US)
Pages (from-to)17-23
Number of pages7
JournalJournal of Magnetic Resonance
Volume245
DOIs
StatePublished - 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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