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Recent developments in MrBUMP: better search-model preparation, graphical interaction with search models, and
Ronan M Keegan1, Stuart J McNicholas2, Jens M H Thomas3
1CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England.
Acta Crystallographica. Section D, Structural Biology
|March 14, 2018
Summary
Molecular replacement (MR) is a key technique in macromolecular crystallography. The MrBUMP pipeline automates MR, incorporating enhanced search models and refinement for difficult structures.
Area of Science:
- Macromolecular X-ray Crystallography
- Structural Biology
- Computational Biology
Background:
- Molecular replacement (MR) is the dominant method for phasing in macromolecular X-ray crystallography.
- Advancements in bioinformatics and refinement techniques have expanded MR's applicability to lower sequence identities.
Purpose of the Study:
- To describe recent developments in the MrBUMP CCP4 pipeline for automating the MR procedure.
- To showcase enhancements in search model sourcing, preparation, and solution refinement.
Main Methods:
- MrBUMP pipeline automation
- Bioinformatic tools for search model sourcing
- Model preparation and ensembling
- Phase improvement and model building
- Online service deployment (CCP4 online)
- Integration with CCP4mg molecular graphics
Main Results:
- MrBUMP automates MR from search model preparation to rebuilding.
- Enhanced tools improve search model identification and preparation.
- Phase improvement and model building address weak MR solutions.
- Online service accelerates solution determination using parallel processing.
Conclusions:
- Recent MrBUMP enhancements improve the automation and success rate of molecular replacement.
- The integrated pipeline and CCP4mg facilitate solving challenging crystallographic structures.
- The online service provides a scalable solution for MR phase determination.
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