ArticleActa crystallographica. Section D, Structural biology2020
ALIXE: a phase-combination tool for fragment-based molecular replacement.
Article in Acta crystallographica. Section D, Structural biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- SFCalculator: connecting deep generative models and crystallography.bioRxiv : the preprint server for biology · 2025Article
- ARCIMBOLDO at low resolution: Verification for coiled coils and globular proteins.Protein science : a publication of the Protein Society · 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
- The CCP4 suite: integrative software for macromolecular crystallography.Acta crystallographica. Section D, Structural biology · 2023Article
- Fragment-BasedACS bio & med chem Au · 2023Article
- The Automatic Solution of Macromolecular Crystal Structures via Molecular Replacement Techniques: REMO22 and Its Pipeline.International journal of molecular sciences · 2023Article
- 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
- Helical ensembles outperform ideal helices in molecular replacement.Acta crystallographica. Section D, Structural biology · 2020Article
- Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER.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
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5 authors.
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Abstract
Fragment-based molecular replacement exploits the use of very accurate yet incomplete search models. In the case of the ARCIMBOLDO programs, consistent phase sets produced from the placement and refinement of fragments with Phaser can be combined in order to increase their signal before proceeding to the step of density modification and autotracing with SHELXE. The program ALIXE compares multiple phase sets, evaluating mean phase differences to determine their common origin, and subsequently produces sets of combined phases that group consistent solutions. In this work, its use on different scenarios of very partial molecular-replacement solutions and its performance after the development of a much-optimized set of algorithms are described. The program is available both standalone and integrated within the ARCIMBOLDO programs. ALIXE has been analysed to identify its rate-limiting steps while exploring the best parameterization to improve its performance and make this software efficient enough to work on modest hardware. The algorithm has been parallelized and redesigned to meet the typical landscape of solutions. Analysis of pairwise correlation between the phase sets has also been explored to test whether this would provide additional insight. ALIXE can be used to exhaustively analyse all partial solutions produced or to complement those already selected for expansion, and also to reduce the number of redundant solutions, which is particularly relevant to the case of coiled coils, or to combine partial solutions from different programs. In each case parallelization and optimization to provide speedup makes its use amenable to typical hardware found in crystallography. ARCIMBOLDO_BORGES and ARCIMBOLDO_SHREDDER now call on ALIXE by default.
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