ArticleJournal of biomolecular NMR2015
Improved reliability, accuracy and quality in automated NMR structure calculation with ARIA.
Article in Journal of biomolecular NMR, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 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
30 citing papers in PubMed, 47 citations in OpenAlex.
- The NMR Exchange Format (NEF): Specification and Applications.bioRxiv : the preprint server for biology · 2026Article
- Impact of Strand Edge N-Amination on the Stability of a Parallel β-Hairpin Fold.The Journal of organic chemistry · 2025Article
- Interplay between CChembiochem : a European journal of chemical biology · 2025Article
- Stabilization of a miniprotein fold by an unpuckered proline surrogate.Communications chemistry · 2025Article
- Backbone Modification in a Protein Hydrophobic Core.Chemistry (Weinheim an der Bergstrasse, Germany) · 2024Article
- Probing effects of site-specific aspartic acid isomerization on structure and stability of GB1 through chemical protein synthesis.Protein science : a publication of the Protein Society · 2024Article
- Structure of the nonhelical filament of the Alzheimer's disease tau core.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Recognition of Histone H3 Methylation States by the PHD1 Domain of Histone Demethylase KDM5A.ACS chemical biology · 2023Article
- Chemical Shifts of Artificial Monomers Used to Construct Heterogeneous-Backbone Protein Mimetics in Random Coil and Folded States.Peptide science (Hoboken, N.J.) · 2023Article
- Facilitating the structural characterisation of non-canonical amino acids in biomolecular NMR.Magnetic resonance (Gottingen, Germany) · 2023Article
- Solution structure of recombinant Pvfp-5β reveals insights into mussel adhesion.Communications biology · 2022Article
- Mechanism of threonine ADP-ribosylation of F-actin by a Tc toxin.Nature communications · 2022Article
- Methyl probes in proteins for determining ligand binding mode in weak protein-ligand complexes.Scientific reports · 2022Article
- A Powassan virus domain III nanoparticle immunogen elicits neutralizing and protective antibodies in mice.PLoS pathogens · 2022Article
- Heterogeneous-Backbone Proteomimetic Analogues of Lasiocepsin, a Disulfide-Rich Antimicrobial Peptide with a Compact Tertiary Fold.ACS chemical biology · 2022Article
- Tandem domain structure determination based on a systematic enumeration of conformations.Scientific reports · 2021Article
- Article
- Endogenous modulators of neurotrophin signaling: Landscape of the transient ATP-NGF interactions.Computational and structural biotechnology journal · 2021Article
- Analysis of folded structure and folding thermodynamics in heterogeneous-backbone proteomimetics.Methods in enzymology · 2021Review
- Proteomimetic Zinc Finger Domains with Modified Metal-binding β-Turns.Peptide science (Hoboken, N.J.) · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In biological NMR, assignment of NOE cross-peaks and calculation of atomic conformations are critical steps in the determination of reliable high-resolution structures. ARIA is an automated approach that performs NOE assignment and structure calculation in a concomitant manner in an iterative procedure. The log-harmonic shape for distance restraint potential and the Bayesian weighting of distance restraints, recently introduced in ARIA, were shown to significantly improve the quality and the accuracy of determined structures. In this paper, we propose two modifications of the ARIA protocol: (1) the softening of the force field together with adapted hydrogen radii, which is meaningful in the context of the log-harmonic potential with Bayesian weighting, (2) a procedure that automatically adjusts the violation tolerance used in the selection of active restraints, based on the fitting of the structure to the input data sets. The new ARIA protocols were fine-tuned on a set of eight protein targets from the CASD-NMR initiative. As a result, the convergence problems previously observed for some targets was resolved and the obtained structures exhibited better quality. In addition, the new ARIA protocols were applied for the structure calculation of ten new CASD-NMR targets in a blind fashion, i.e. without knowing the actual solution. Even though optimisation of parameters and pre-filtering of unrefined NOE peak lists were necessary for half of the targets, ARIA consistently and reliably determined very precise and highly accurate structures for all cases. In the context of integrative structural biology, an increasing number of experimental methods are used that produce distance data for the determination of 3D structures of macromolecules, stressing the importance of methods that successfully make use of ambiguous and noisy distance data.
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.