ArticleProtein science : a publication of the Protein Society2021
Crystallographic molecular replacement using an in silico-generated search model of SARS-CoV-2 ORF8.
Article in Protein science : a publication of the Protein Society, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed.
- Bridging structure and function: artificial intelligence-based modelling of kidney proteins.Nature reviews. Nephrology · 2026Review
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- AlphaFold-predicted protein structures and small-angle X-ray scattering: insights from an extended examination of selected data in the Small-Angle Scattering Biological Data Bank.Journal of applied crystallography · 2023Article
- Crystal structure of the monocupin ring-cleaving dioxygenase 5-nitrosalicylate 1,2-dioxygenase from Bradyrhizobium sp.Acta crystallographica. Section D, Structural biology · 2023Article
- Beyond the US-SOMO-AF database: a new website for hydrodynamic, structural, and circular dichroism calculations on user-supplied structures.European biophysics journal : EBJ · 2023Article
- Using AlphaFold Predictions in Viral Research.Current issues in molecular biology · 2023Review
- E6AP AZUL interaction with UBQLN1/2 in cells, condensates, and an AlphaFold-NMR integrated structure.Structure (London, England : 1993) · 2023Article
- The opportunities and challenges posed by the new generation of deep learning-based protein structure predictors.Current opinion in structural biology · 2023Review
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- AlphaFold accelerates artificial intelligence powered drug discovery: efficient discovery of a novel CDK20 small molecule inhibitor.Chemical science · 2023Article
- Using AlphaFold to predict the impact of single mutations on protein stability and function.PloS one · 2023Article
- The impact of AlphaFold2 on experimental structure solution.Faraday discussions · 2022Article
- Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2.Chemical reviews · 2022Review
- Structural Comparison and Drug Screening of Spike Proteins of Ten SARS-CoV-2 Variants.Research (Washington, D.C.) · 2022Article
- Genome-wide analysis of theFrontiers in plant science · 2022Article
- The integration of AlphaFold-predicted and crystal structures of humanComputational and structural biotechnology journal · 2022Article
- An Overview of Alphafold's Breakthrough.Frontiers in artificial intelligence · 2022Review
- Implications of AlphaFold2 for crystallographic phasing by molecular replacement.Acta crystallographica. Section D, Structural biology · 2022Review
- Article
- Crystallographic molecular replacement using an in silico-generated search model of SARS-CoV-2 ORF8.Protein science : a publication of the Protein Society · 2021Article
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Abstract
The majority of crystal structures are determined by the method of molecular replacement (MR). The range of application of MR is limited mainly by the need for an accurate search model. In most cases, pre-existing experimentally determined structures are used as search models. In favorable cases, ab initio predicted structures have yielded search models adequate for MR. The ORF8 protein of SARS-CoV-2 represents a challenging case for MR using an ab initio prediction because ORF8 has an all β-sheet fold and few orthologs. We previously determined experimentally the structure of ORF8 using the single anomalous dispersion (SAD) phasing method, having been unable to find an MR solution to the crystallographic phase problem. Following a report of an accurate prediction of the ORF8 structure, we assessed whether the predicted model would have succeeded as an MR search model. A phase problem solution was found, and the resulting structure was refined, yielding structural parameters equivalent to the original experimental solution.
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