ArticleActa crystallographica. Section D, Structural biology2018
Recent developments in MrBUMP: better search-model preparation, graphical interaction with search models, and solution improvement and assessment.
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 26 papers.
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26 citing papers in PubMed.
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- Modes and model building in SHELXE.Acta crystallographica. Section D, Structural biology · 2024Article
- 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
- MrParse: finding homologues in the PDB and the EBI AlphaFold database for molecular replacement and more.Acta crystallographica. Section D, Structural biology · 2022Article
- Structure-guided mutagenesis of a mucin-selective metalloprotease from Akkermansia muciniphila alters substrate preferences.The Journal of biological chemistry · 2022Article
- The integration of AlphaFold-predicted and crystal structures of humanComputational and structural biotechnology journal · 2022Article
- The X-ray structure of juvenile hormone diol kinase from the silkworm Bombyx mori.Acta crystallographica. Section F, Structural biology communications · 2021Article
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- Redeployment of automated MrBUMP search-model identification for map fitting in cryo-EM.Acta crystallographica. Section D, Structural biology · 2021Article
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- Introduction to molecular replacement: a time perspective.Acta crystallographica. Section D, Structural biology · 2021Review
- The accuracy of protein models automatically built into cryo-EM maps with ARP/wARP.Acta crystallographica. Section D, Structural biology · 2021Article
- The copper(II)-binding tripeptide GHK, a valuable crystallization and phasing tag for macromolecular crystallography.Acta crystallographica. Section D, Structural biology · 2020Article
- Uncovering a novel molecular mechanism for scavenging sialic acids in bacteria.The Journal of biological chemistry · 2020Article
- Helical ensembles outperform ideal helices in molecular replacement.Acta crystallographica. Section D, Structural biology · 2020Article
- Extending the scope of coiled-coil crystal structure solution by AMPLE through improved ab initio modelling.Acta crystallographica. Section D, Structural biology · 2020Article
- Using Phaser and ensembles to improve the performance of SIMBAD.Acta crystallographica. Section D, Structural biology · 2020Article
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Abstract
Increasing sophistication in molecular-replacement (MR) software and the rapid expansion of the PDB in recent years have allowed the technique to become the dominant method for determining the phases of a target structure in macromolecular X-ray crystallography. In addition, improvements in bioinformatic techniques for finding suitable homologous structures for use as MR search models, combined with developments in refinement and model-building techniques, have pushed the applicability of MR to lower sequence identities and made weak MR solutions more amenable to refinement and improvement. MrBUMP is a CCP4 pipeline which automates all stages of the MR procedure. Its scope covers everything from the sourcing and preparation of suitable search models right through to rebuilding of the positioned search model. Recent improvements to the pipeline include the adoption of more sensitive bioinformatic tools for sourcing search models, enhanced model-preparation techniques including better ensembling of homologues, and the use of phase improvement and model building on the resulting solution. The pipeline has also been deployed as an online service through CCP4 online, which allows its users to exploit large bioinformatic databases and coarse-grained parallelism to speed up the determination of a possible solution. Finally, the molecular-graphics application CCP4mg has been combined with MrBUMP to provide an interactive visual aid to the user during the process of selecting and manipulating search models for use in MR. Here, these developments in MrBUMP are described with a case study to explore how some of the enhancements to the pipeline and to CCP4mg can help to solve a difficult case.
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