ArticleNature communications2020
A method for validating the accuracy of NMR protein structures.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Crystal structure of human Dickkopf 4 cysteine-rich domain 1 and evaluation of conformational rigidity.Acta crystallographica. Section F, Structural biology communications · 2026Article
- Experiment-guided AlphaFold3 resolves measurement-consistent protein ensembles.Nature biotechnology · 2026Article
- Hidden structural states of proteins revealed by conformer selection.Nature communications · 2026Article
- PEPNet: a two-stage point cloud framework with hierarchical embedding and antigen-antibody interaction modeling for epitope prediction.Briefings in bioinformatics · 2026Article
- X-ray absorption spectroscopy of lanmodulin-derived peptides bound to rare earth elements.Journal of synchrotron radiation · 2025Article
- Assisting and accelerating NMR assignment with restrained structure prediction.Communications biology · 2025Article
- NMR Spectroscopy for the Validation of AlphaFold2 Structures.bioRxiv : the preprint server for biology · 2025Article
- WUREN: Whole-modal union representation for epitope prediction.Computational and structural biotechnology journal · 2024Article
- UCBShift 2.0: Bridging the Gap from Backbone to Side Chain Protein Chemical Shift Prediction for Protein Structures.Journal of the American Chemical Society · 2024Article
- Assessment of Four Theoretical Approaches to Predict Protein Flexibility in the Crystal Phase and Solution.Journal of chemical theory and computation · 2024Article
- Exploring protein functions from structural flexibility using CABS-flex modeling.Protein science : a publication of the Protein Society · 2024Review
- De novo generation of SARS-CoV-2 antibody CDRH3 with a pre-trained generative large language model.Nature communications · 2024Article
- Restraint validation of biomolecular structures determined by NMR in the Protein Data Bank.Structure (London, England : 1993) · 2024Article
- MoDAFold: a strategy for predicting the structure of missense mutant protein based on AlphaFold2 and molecular dynamics.Briefings in bioinformatics · 2024Article
- Structure, dynamics, and stability of the smallest and most complex 7The Journal of biological chemistry · 2024Article
- A practical guide to machine-learning scoring for structure-based virtual screening.Nature protocols · 2023Review
- Identification of Two Flip-Over Genes in Grass Family as Potential Signature of C4 Photosynthesis Evolution.International journal of molecular sciences · 2023Article
- The history and conceptual framework of assays and screens.BioEssays : news and reviews in molecular, cellular and developmental biology · 2023Article
- Rapid protein assignments and structures from raw NMR spectra with the deep learning technique ARTINA.Nature communications · 2022Article
- Local Backbone Geometry Plays a Critical Role in Determining Conformational Preferences of Amino Acid Residues in Proteins.Biomolecules · 2022Article
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3 authors.
Funding
Abstract
We present a method that measures the accuracy of NMR protein structures. It compares random coil index [RCI] against local rigidity predicted by mathematical rigidity theory, calculated from NMR structures [FIRST], using a correlation score (which assesses secondary structure), and an RMSD score (which measures overall rigidity). We test its performance using: structures refined in explicit solvent, which are much better than unrefined structures; decoy structures generated for 89 NMR structures; and conventional predictors of accuracy such as number of restraints per residue, restraint violations, energy of structure, ensemble RMSD, Ramachandran distribution, and clashscore. Restraint violations and RMSD are poor measures of accuracy. Comparisons of NMR to crystal structures show that secondary structure is equally accurate, but crystal structures are typically too rigid in loops, whereas NMR structures are typically too floppy overall. We show that the method is a useful addition to existing measures of accuracy.
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