ArticleActa crystallographica. Section D, Structural biology2018
Exploiting distant homologues for phasing through the generation of compact fragments, local fold refinement and partial solution combination.
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 23 papers.
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Who cites it
23 citing papers in PubMed.
- Scotty: lattice coincidences for macromolecular crystallographic phasing.Acta crystallographica. Section D, Structural biology · 2026Article
- ARCIMBOLDO at low resolution: Verification for coiled coils and globular proteins.Protein science : a publication of the Protein Society · 2024Article
- Molecular and structural basis of oligopeptide recognition by the Ami transporter system in pneumococci.PLoS pathogens · 2024Article
- Modes and model building in SHELXE.Acta crystallographica. Section D, Structural biology · 2024Article
- Article
- Predicted models and CCP4.Acta crystallographica. Section D, Structural biology · 2023Article
- Fragment-BasedACS bio & med chem Au · 2023Article
- Article
- Verification: model-free phasing with enhanced predicted models in ARCIMBOLDO_SHREDDER.Acta crystallographica. Section D, Structural biology · 2022Article
- SPACA6 ectodomain structure reveals a conserved superfamily of gamete fusion-associated proteins.Communications biology · 2022Article
- Implications of AlphaFold2 for crystallographic phasing by molecular replacement.Acta crystallographica. Section D, Structural biology · 2022Review
- Phasertng: directed acyclic graphs for crystallographic phasing.Acta crystallographica. Section D, Structural biology · 2021Article
- Structural characterization of anti-CCL5 activity of the tick salivary protein evasin-4.The Journal of biological chemistry · 2020Article
- Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER.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
- ALIXE: a phase-combination tool for fragment-based molecular replacement.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
- Identification of the active site residues in ATP-citrate lyase's carboxy-terminal portion.Protein science : a publication of the Protein Society · 2019Article
- Ega3 from the fungal pathogenThe Journal of biological chemistry · 2019Article
- Structure and assembly of pilotin-dependent and -independent secretins of the type II secretion system.PLoS pathogens · 2019Article
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10 authors.
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Abstract
Macromolecular structures can be solved by molecular replacement provided that suitable search models are available. Models from distant homologues may deviate too much from the target structure to succeed, notwithstanding an overall similar fold or even their featuring areas of very close geometry. Successful methods to make the most of such templates usually rely on the degree of conservation to select and improve search models. ARCIMBOLDO_SHREDDER uses fragments derived from distant homologues in a brute-force approach driven by the experimental data, instead of by sequence similarity. The new algorithms implemented in ARCIMBOLDO_SHREDDER are described in detail, illustrating its characteristic aspects in the solution of new and test structures. In an advance from the previously published algorithm, which was based on omitting or extracting contiguous polypeptide spans, model generation now uses three-dimensional volumes respecting structural units. The optimal fragment size is estimated from the expected log-likelihood gain (LLG) values computed assuming that a substructure can be found with a level of accuracy near that required for successful extension of the structure, typically below 0.6 Å root-mean-square deviation (r.m.s.d.) from the target. Better sampling is attempted through model trimming or decomposition into rigid groups and optimization through Phaser's gyre refinement. Also, after model translation, packing filtering and refinement, models are either disassembled into predetermined rigid groups and refined (gimble refinement) or Phaser's LLG-guided pruning is used to trim the model of residues that are not contributing signal to the LLG at the target r.m.s.d. value. Phase combination among consistent partial solutions is performed in reciprocal space with ALIXE. Finally, density modification and main-chain autotracing in SHELXE serve to expand to the full structure and identify successful solutions. The performance on test data and the solution of new structures are described.
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