ArticleActa crystallographica. Section D, Structural biology2018
Model validation: local diagnosis, correction and when to quit.
Article in Acta crystallographica. Section D, Structural biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
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- The Untangle Challenge for accurate ensemble models.bioRxiv : the preprint server for biology · 2026Article
- Cat_Wiz: a stereochemistry-guided toolkit for locating, diagnosing, and annotating Mg2+ ions in RNA structures.Nucleic acids research · 2026Article
- New targets and procedures for validating the valence geometry of nucleic acid structures.Nucleic acids research · 2026Article
- AstraMEV (AI-Guided Structural Assembly of Multi-Epitope Vaccines) Against Infectious Bronchitis Virus.Journal of chemical information and modeling · 2025Article
- AQuaRef: machine learning accelerated quantum refinement of protein structures.Nature communications · 2025Article
- Structural Prediction of Coronavirus s2m Kissing Complexes and Extended Duplexes.ACS physical chemistry Au · 2025Article
- De Novo Hydration of Cryo-EM Reconstructions through Molecular Dynamics Simulations of the Excess Chemical Potential.bioRxiv : the preprint server for biology · 2025Article
- Article
- Structural determination and kinetic analysis of the transketolase from Vibrio vulnificus reveal unexpected cooperative behavior.Protein science : a publication of the Protein Society · 2024Article
- Atg18 oligomer organization in assembled tubes and on lipid membrane scaffolds.Nature communications · 2023Article
- The bad and the good of trends in model building and refinement for sparse-data regions: pernicious forms of overfitting versus good new tools and predictions.Acta crystallographica. Section D, Structural biology · 2023Article
- Distance-based global analysis of consistentHeliyon · 2023Article
- Overall protein structure quality assessment using hydrogen-bonding parameters.Acta crystallographica. Section D, Structural biology · 2023Article
- FLEXR: automated multi-conformer model building using electron-density map sampling.Acta crystallographica. Section D, Structural biology · 2023Article
- CERES: a cryo-EM re-refinement system for continuous improvement of deposited models.Acta crystallographica. Section D, Structural biology · 2021Article
- A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry.Structure (London, England : 1993) · 2020Article
- Nature of the copper-nitrosyl intermediates of copper nitrite reductases during catalysis.Chemical science · 2020Article
- ALEPH: a network-oriented approach for the generation of fragment-based libraries and for structure interpretation.Acta crystallographica. Section D, Structural biology · 2020Article
Corrections and comments
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7 authors.
Funding
Abstract
Traditionally, validation was considered to be a final gatekeeping function, but refinement is smoother and results are better if model validation actively guides corrections throughout structure solution. This shifts emphasis from global to local measures: primarily geometry, conformations and sterics. A fit into the wrong local minimum conformation usually produces outliers in multiple measures. Moving to the right local minimum should be prioritized, rather than small shifts across arbitrary borderlines. Steric criteria work best with all explicit H atoms. `Backrub' motions should be used for side chains and `P-perp' diagnostics to correct ribose puckers. A `water' may actually be an ion, a relic of misfitting or an unmodeled alternate. Beware of wishful thinking in modeling ligands. At high resolution, internally consistent alternate conformations should be modeled and geometry in poor density should not be downweighted. At low resolution, CaBLAM should be used to diagnose protein secondary structure and ERRASER to correct RNA backbone. All atoms should not be forced inside density, beware of sequence misalignment, and very rare conformations such as cis-non-Pro peptides should be avoided. Automation continues to improve, but the crystallographer still must look at each outlier, in the context of density, and correct most of them. For the valid few with unambiguous density and something that is holding them in place, a functional reason should be sought. The expectation is a few outliers, not zero.
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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.