ArticleJournal of magnetic resonance (San Diego, Calif. : 1997)2014
FLAMEnGO 2.0: an enhanced fuzzy logic algorithm for structure-based assignment of methyl group resonances.
Article in Journal of magnetic resonance (San Diego, Calif. : 1997), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- AMIGO - Guided assignment ofJournal of biomolecular NMR · 2026Article
- A fast and efficient strategy for the NMR assignment of Fab methyl groups.Journal of biomolecular NMR · 2026Article
- NMR chemical shift assignment of the IMLV methyl groups of a di-domain of the Tomaymycin non-ribosomal peptide synthetase.Biomolecular NMR assignments · 2025Article
- Leveraging AlphaFold2 and residual dipolar couplings for side-chain methyl group assignment: A case study with S. cerevisiae Xrs2.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2025Article
- Synthesis ofOrganic & biomolecular chemistry · 2023Article
- Robust automated backbone triple resonance NMR assignments of proteins using Bayesian-based simulated annealing.Nature communications · 2023Article
- ATP-competitive inhibitors modulate the substrate binding cooperativity of a kinase by altering its conformational entropy.Science advances · 2022Article
- Ligand-induced structural transitions combined with paramagnetic ions facilitate unambiguous NMR assignments of methyl groups in large proteins.Journal of biomolecular NMR · 2022Article
- Progress toward automated methyl assignments for methyl-TROSY applications.Structure (London, England : 1993) · 2022Article
- Optimized precursor to simplify assignment transfer between backbone resonances and stereospecifically labelled valine and leucine methyl groups: application to human Hsp90 N-terminal domain.Journal of biomolecular NMR · 2021Article
- Backbone-independent NMR resonance assignments of methyl probes in large proteins.Nature communications · 2021Article
- Nearest-neighbor NMR spectroscopy: categorizing spectral peaks by their adjacent nuclei.Nature communications · 2020Article
- Spectral editing of intra- and inter-chain methyl-methyl NOEs in protein complexes.Journal of biomolecular NMR · 2020Article
- Automatic structure-based NMR methyl resonance assignment in large proteins.Nature communications · 2019Article
- Globally correlated conformational entropy underlies positive and negative cooperativity in a kinase's enzymatic cycle.Nature communications · 2019Article
- Assigning methyl resonances for protein solution-state NMR studies.Methods (San Diego, Calif.) · 2018Article
- Complete assignment of Ala, Ile, Leu, Met and Val methyl groups of human blood group A and B glycosyltransferases using lanthanide-induced pseudocontact shifts and methyl-methyl NOESY.Journal of biomolecular NMR · 2018Article
- Automatic methyl assignment in large proteins by the MAGIC algorithm.Journal of biomolecular NMR · 2017Article
- Methyl group assignment using pseudocontact shifts with PARAssign.Journal of biomolecular NMR · 2017Article
- NMR assignments of sparsely labeled proteins using a genetic algorithm.Journal of biomolecular NMR · 2017Article
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6 authors.
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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.
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