ArticleActa crystallographica. Section D, Structural biology2022
Putting AlphaFold models to work with phenix.process_predicted_model and ISOLDE.
Article in Acta crystallographica. Section D, Structural biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
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- Automated assembly of protein complexes from cryo-EM maps with structure-informed Monte Carlo Tree Search.bioRxiv : the preprint server for biology · 2026Article
- Signaling mechanism of the transmembrane energy receptor Aer.bioRxiv : the preprint server for biology · 2026Article
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- Alphafuser: a parsimonious approach to predicting higher-order protein complexes.Acta crystallographica. Section D, Structural biology · 2026Article
- Cryo-EM Structure of Human ATAD2B Reveals a Hexameric Organization Contributes to ATPase Activity and Substrate Coordination.bioRxiv : the preprint server for biology · 2026Article
- Model Quality Assessment for CASP16.Proteins · 2026Article
- Cryo-EM Analysis in CASP16.Proteins · 2026Article
- Spatial constraints drive amylosome-mediated resistant starch degradation by Ruminococcus bromii in the human colon.Nature communications · 2025Article
- Dissimilar Reactions and Enzymes for Psilocybin Biosynthesis in Inocybe and Psilocybe Mushrooms.Angewandte Chemie (International ed. in English) · 2025Article
- Structure and function of otoferlin, a synaptic protein of sensory hair cells essential for hearing.Science advances · 2025Article
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- Structural insights into lipid membrane binding by human ferlins.The EMBO journal · 2025Article
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- A new age in structural S-layer biology: Experimental and in silico milestones.The Journal of biological chemistry · 2025Review
- Emerging frontiers in protein structure prediction following the AlphaFold revolution.Journal of the Royal Society, Interface · 2025Review
- Slice'N'Dice: maximizing the value of predicted models for structural biologists.Acta crystallographica. Section D, Structural biology · 2025Article
- An outlook on structural biology after AlphaFold: tools, limits and perspectives.FEBS open bio · 2025Review
- Structural and functional prediction, evaluation, and validation in the post-sequencing era.Computational and structural biotechnology journal · 2024Review
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7 authors.
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Abstract
AlphaFold has recently become an important tool in providing models for experimental structure determination by X-ray crystallography and cryo-EM. Large parts of the predicted models typically approach the accuracy of experimentally determined structures, although there are frequently local errors and errors in the relative orientations of domains. Importantly, residues in the model of a protein predicted by AlphaFold are tagged with a predicted local distance difference test score, informing users about which regions of the structure are predicted with less confidence. AlphaFold also produces a predicted aligned error matrix indicating its confidence in the relative positions of each pair of residues in the predicted model. The phenix.process_predicted_model tool downweights or removes low-confidence residues and can break a model into confidently predicted domains in preparation for molecular replacement or cryo-EM docking. These confidence metrics are further used in ISOLDE to weight torsion and atom-atom distance restraints, allowing the complete AlphaFold model to be interactively rearranged to match the docked fragments and reducing the need for the rebuilding of connecting regions.
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