ArticleJournal of biomolecular NMR2017
Automatic methyl assignment in large proteins by the MAGIC algorithm.
Article in Journal of biomolecular NMR, 2017. 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
- Mechanisms of assembly and function of the Hsp70-Hsp40 chaperone machinery.Molecular cell · 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
- Efficient and economic protein labeling for NMR in mammalian expression systems: Application to a preT-cell and T-cell receptor protein.Protein science : a publication of the Protein Society · 2024Article
- Synthesis ofOrganic & biomolecular chemistry · 2023Article
- Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.Journal of the American Chemical Society · 2023Article
- Robust automated backbone triple resonance NMR assignments of proteins using Bayesian-based simulated annealing.Nature communications · 2023Article
- An NMR look at an engineered PET depolymerase.Biophysical journal · 2022Article
- Ligand-induced structural transitions combined with paramagnetic ions facilitate unambiguous NMR assignments of methyl groups in large proteins.Journal of biomolecular NMR · 2022Article
- Structural basis for the inhibition of IAPP fibril formation by the co-chaperonin prefoldin.Nature communications · 2022Article
- Imatinib can act as an Allosteric Activator of Abl Kinase.Journal of molecular biology · 2022Article
- Progress toward automated methyl assignments for methyl-TROSY applications.Structure (London, England : 1993) · 2022Article
- Article
- 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
- Molecular basis for the allosteric activation mechanism of the heterodimeric imidazole glycerol phosphate synthase complex.Nature communications · 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
- Conformational states dynamically populated by a kinase determine its function.Science (New York, N.Y.) · 2020Article
- Spectral editing of intra- and inter-chain methyl-methyl NOEs in protein complexes.Journal of biomolecular NMR · 2020Article
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Authors and funding
9 authors.
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Abstract
Selective methyl labeling is an extremely powerful approach to study the structure, dynamics and function of biomolecules by NMR. Despite spectacular progress in the field, such studies remain rather limited in number. One of the main obstacles remains the assignment of the methyl resonances, which is labor intensive and error prone. Typically, NOESY crosspeak patterns are manually correlated to the available crystal structure or an in silico template model of the protein. Here, we propose methyl assignment by graphing inference construct, an exhaustive search algorithm with no peak network definition requirement. In order to overcome the combinatorial problem, the exhaustive search is performed locally, i.e. for a small number of methyls connected through-space according to experimental 3D methyl NOESY data. The local network approach drastically reduces the search space. Only the best local assignments are combined to provide the final output. Assignments that match the data with comparable scores are made available to the user for cross-validation by additional experiments such as methyl-amide NOEs. Several NMR datasets for proteins in the 25-50 kDa range were used during development and for performance evaluation against the manually assigned data. We show that the algorithm is robust, reliable and greatly speeds up the methyl assignment task.
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