ArticleActa crystallographica. Section D, Structural biology2024
The success rate of processed predicted models in molecular replacement: implications for experimental phasing in the AlphaFold era.
Article in Acta crystallographica. Section D, Structural biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- From mechanistic modeling to AI-driven design: computational strategies for targeting the γ-secretase complex.Briefings in bioinformatics · 2026Review
- Structural basis of a 2-oxoglutarate-dependent heme-oxygenase-like enzyme HamA in fragin biosynthesis.RSC advances · 2025Article
- Evolution of macromolecular crystallography beamlines at the Swiss Light Source and SwissFEL.Journal of synchrotron radiation · 2025Article
- Article
- Project automation in CCP4 Cloud: Enabling customization and high-throughput efficiency.Protein science : a publication of the Protein Society · 2025Article
- Crystallization and initial X-ray crystallographic analysis of a de novo-designed protein with left-handed βαβ units.Acta crystallographica. Section F, Structural biology communications · 2025Article
- Slice'N'Dice: maximizing the value of predicted models for structural biologists.Acta crystallographica. Section D, Structural biology · 2025Article
- SFCalculator: connecting deep generative models and crystallography.bioRxiv : the preprint server for biology · 2025Article
- Multimeric protein interaction and complex prediction: Structure, dynamics and function.Computational and structural biotechnology journal · 2025Review
- ABCFold: easier running and comparison of AlphaFold 3, Boltz-1, and Chai-1.Bioinformatics advances · 2025Article
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3 authors.
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Abstract
The availability of highly accurate protein structure predictions from AlphaFold2 (AF2) and similar tools has hugely expanded the applicability of molecular replacement (MR) for crystal structure solution. Many structures can be solved routinely using raw models, structures processed to remove unreliable parts or models split into distinct structural units. There is therefore an open question around how many and which cases still require experimental phasing methods such as single-wavelength anomalous diffraction (SAD). Here, this question is addressed using a large set of PDB depositions that were solved by SAD. A large majority (87%) could be solved using unedited or minimally edited AF2 predictions. A further 18 (4%) yield straightforwardly to MR after splitting of the AF2 prediction using Slice'N'Dice, although different splitting methods succeeded on slightly different sets of cases. It is also found that further unique targets can be solved by alternative modelling approaches such as ESMFold (four cases), alternative MR approaches such as ARCIMBOLDO and AMPLE (two cases each), and multimeric model building with AlphaFold-Multimer or UniFold (three cases). Ultimately, only 12 cases, or 3% of the SAD-phased set, did not yield to any form of MR tested here, offering valuable hints as to the number and the characteristics of cases where experimental phasing remains essential for macromolecular structure solution.
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