ArticleActa crystallographica. Section D, Structural biology2018
Fragon: rapid high-resolution structure determination from ideal protein fragments.
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 21 papers.
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Who cites it
21 citing papers in PubMed.
- Direct from the seed: an atomic resolution protein structure by ab initio MicroED.Nature communications · 2026Article
- ARCIMBOLDO at low resolution: Verification for coiled coils and globular proteins.Protein science : a publication of the Protein Society · 2024Article
- Structural Characterization of Disulfide-Linked p53-Derived Peptide Dimers.Research square · 2024Article
- Predicted models and CCP4.Acta crystallographica. Section D, Structural biology · 2023Article
- Polymorphic amyloid nanostructures of hormone peptides involved in glucose homeostasis display reversible amyloid formation.Nature communications · 2023Article
- The CCP4 suite: integrative software for macromolecular crystallography.Acta crystallographica. Section D, Structural biology · 2023Article
- From peptides to proteins: coiled-coil tetramers to single-chain 4-helix bundles.Chemical science · 2022Article
- Ab initio phasing macromolecular structures using electron-counted MicroED data.Nature methods · 2022Article
- Periscope Proteins are variable-length regulators of bacterial cell surface interactions.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Structure of a GH51 α-L-arabinofuranosidase from Meripilus giganteus: conserved substrate recognition from bacteria to fungi.Acta crystallographica. Section D, Structural biology · 2020Article
- Helical ensembles outperform ideal helices in molecular replacement.Acta crystallographica. Section D, Structural biology · 2020Article
- Article
- Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER.Acta crystallographica. Section D, Structural biology · 2020Article
- The use of local structural similarity of distant homologues for crystallographic model building from a molecular-replacement solution.Acta crystallographica. Section D, Structural biology · 2020Article
- ALEPH: a network-oriented approach for the generation of fragment-based libraries and for structure interpretation.Acta crystallographica. Section D, Structural biology · 2020Article
- SEQUENCE SLIDER: expanding polyalanine fragments for phasing with multiple side-chain hypotheses.Acta crystallographica. Section D, Structural biology · 2020Article
- Molecular replacement using structure predictions from databases.Acta crystallographica. Section D, Structural biology · 2019Article
- Ab initio structure solution of a proteolytic fragment using ARCIMBOLDO.Acta crystallographica. Section F, Structural biology communications · 2018Article
- SIMBAD: a sequence-independent molecular-replacement pipeline.Acta crystallographica. Section D, Structural biology · 2018Article
- Recent developments in MrBUMP: better search-model preparation, graphical interaction with search models, and solution improvement and assessment.Acta crystallographica. Section D, Structural biology · 2018Article
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Abstract
Correctly positioning ideal protein fragments by molecular replacement presents an attractive method for obtaining preliminary phases when no template structure for molecular replacement is available. This has been exploited in several existing pipelines. This paper presents a new pipeline, named Fragon, in which fragments (ideal α-helices or β-strands) are placed using Phaser and the phases calculated from these coordinates are then improved by the density-modification methods provided by ACORN. The reliable scoring algorithm provided by ACORN identifies success. In these cases, the resulting phases are usually of sufficient quality to enable automated model building of the entire structure. Fragon was evaluated against two test sets comprising mixed α/β folds and all-β folds at resolutions between 1.0 and 1.7 Å. Success rates of 61% for the mixed α/β test set and 30% for the all-β test set were achieved. In almost 70% of successful runs, fragment placement and density modification took less than 30 min on relatively modest four-core desktop computers. In all successful runs the best set of phases enabled automated model building with ARP/wARP to complete the structure.
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