ArticleActa crystallographica. Section D, Structural biology2020
Using Phaser and ensembles to improve the performance of SIMBAD.
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 9 papers.
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Who cites it
9 citing papers in PubMed.
- Cryo-EM reveals ArnA contamination during purification of a ciliary protein complex.Acta crystallographica. Section D, Structural biology · 2026Article
- Protein crystallization and structure determination at room temperature in the CrystalChip.FEBS open bio · 2025Article
- The CCP4 suite: integrative software for macromolecular crystallography.Acta crystallographica. Section D, Structural biology · 2023Article
- Identification, structure determination and analysis of Mycobacterium smegmatis acyl-carrier protein synthase (AcpS) crystallized serendipitously.Acta crystallographica. Section F, Structural biology communications · 2022Article
- Article
- Introduction to molecular replacement: a time perspective.Acta crystallographica. Section D, Structural biology · 2021Review
- Helical ensembles outperform ideal helices in molecular replacement.Acta crystallographica. Section D, Structural biology · 2020Article
- Molecular replacement using structure predictions from databases.Acta crystallographica. Section D, Structural biology · 2019Article
- 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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11 authors.
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Abstract
The conventional approach to search-model identification in molecular replacement (MR) is to screen a database of known structures using the target sequence. However, this strategy is not always effective, for example when the relationship between sequence and structural similarity fails or when the crystal contents are not those expected. An alternative approach is to identify suitable search models directly from the experimental data. SIMBAD is a sequence-independent MR pipeline that uses either a crystal lattice search or MR functions to directly locate suitable search models from databases. The previous version of SIMBAD used the fast AMoRe rotation-function search. Here, a new version of SIMBAD which makes use of Phaser and its likelihood scoring to improve the sensitivity of the pipeline is presented. It is shown that the additional compute time potentially required by the more sophisticated scoring is counterbalanced by the greater sensitivity, allowing more cases to trigger early-termination criteria, rather than running to completion. Using Phaser solved 17 out of 25 test cases in comparison to the ten solved with AMoRe, and it is shown that use of ensemble search models produces additional performance benefits.
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