ArticleJournal of biomolecular NMR2013
MAP-XSII: an improved program for the automatic assignment of methyl resonances in large proteins.
Article in Journal of biomolecular NMR, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
26 citing papers in PubMed, 43 citations in OpenAlex.
- 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
- 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
- Robust automated backbone triple resonance NMR assignments of proteins using Bayesian-based simulated annealing.Nature communications · 2023Article
- 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
- 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
- Methyl group assignment using pseudocontact shifts with PARAssign.Journal of biomolecular NMR · 2017Article
- Automatic methyl assignment in large proteins by the MAGIC algorithm.Journal of biomolecular NMR · 2017Article
- Automated assignment of NMR chemical shifts based on a known structure and 4D spectra.Journal of biomolecular NMR · 2016Article
- Exploiting E. coli auxotrophs for leucine, valine, and threonine specific methyl labeling of large proteins for NMR applications.Journal of biomolecular NMR · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
NMR studies of large proteins have gathered much interest in recent years, especially after methyl-transverse relaxation optimized spectroscopy was successfully applied to systems as large as ~1 MDa in molecular weight. However, to fully take advantage of these spectra, there is a need for convenient and robust methods for making resonance assignments rapidly. Here, we present an improved version of our program MAP-XS (methyl assignment prediction from X-ray structure) for the automatic assignment of methyl peaks, based on nuclear Overhauser effects (NOE) correlations and chemical shifts together with available structures. No manual analysis of the NOE data is needed in this new version, which helps to further accelerate the assignment process. A refined algorithm as well as more efficient sampling produces results from single runs of MAP-XSII using unanalyzed NOE data are comparable to those achieved by the old version using manually curated data with every NOE peak correctly attributed to the two related methyl peaks; in addition, checking the results from multiple parallel runs against each other provides an effective mechanism for getting rid of the wrong assignments while keeping the correct ones, which significantly improves the reliability of final assignments. The new program is tested against three different proteins and delivers ~95 % correct assignments; positive results are also achieved for tests using different cut-off distances for NOEs, structures of lower resolutions, and ambiguous residue types.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.