ArticleProtein science : a publication of the Protein Society2024
Xplor-NIH: Better parameters and protocols for NMR protein structure determination.
Article in Protein science : a publication of the Protein Society, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Interaction of Bacterial Histidine Phosphatase SixA With Phosphocarrier Protein NPr and Phosphohistidine Analogs.Journal of molecular biology · 2026Article
- Molecular modelling of the adipokinetic hormone receptor from the stick insect Carausius morosus, and its endogenous agonist.Scientific reports · 2026Article
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- Untangling or further entangling? Theoretical expansion of the structural landscape of nucleic acid quadruplexes and modeling with 3D-NuS-Qplex.Briefings in bioinformatics · 2026Article
- The NMR Exchange Format (NEF): Specification and Applications.bioRxiv : the preprint server for biology · 2026Article
- Article
- Mesostructured Water Enhances Stability of ProteinMPNN-Designed Ubiquitin-Fold Proteins.Journal of the American Chemical Society · 2026Article
- Diverse regulation of functional dimerization of a sugar transporter by different interfacial lipids.Nature communications · 2026Article
- In-situ cross-linking mass spectrometry reveals compartment-specific proteasomal interactions and structural heterogeneity.Nature communications · 2025Article
- Zinc-Induced Folding and Solution Structure of the Eponymous Novel Zinc Finger from the ZC4H2 Protein.Biomolecules · 2025Article
- Solution structure of the Z0 domain from transcription repressor BCL11A sheds light on the sequence properties of protein-binding zinc fingers.Protein science : a publication of the Protein Society · 2025Article
- Formerly degenerate seventh zinc finger domain from transcription factor ZNF711 rehabilitated by experimental NMR structure.Protein science : a publication of the Protein Society · 2024Article
- Xplor-NIH: Better parameters and protocols for NMR protein structure determination.Protein science : a publication of the Protein Society · 2024Article
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Authors and funding
4 authors.
Funding
Abstract
The present work describes an update to the protein covalent geometry and atomic radii parameters in the Xplor-NIH biomolecular structure determination package. In combination with an improved treatment of selected non-bonded interactions between atoms three bonds apart, such as those involving methyl hydrogens, and a previously developed term that affects the system's gyration volume, the new parameters are tested using structure calculations on 30 proteins with restraints derived from nuclear magnetic resonance data. Using modern structure validation criteria, including several formally adopted by the Protein Data Bank, and a clear measure of structural accuracy, the results show superior performance relative to previous Xplor-NIH implementations. Additionally, the Xplor-NIH structures compare favorably against originally determined NMR models.
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