Simpkin, Adam J, Winn, Martyn D, Rigden, Daniel J 
ORCID: 0000-0002-7565-8937 and Keegan, Ronan M
(2021)
Redeployment of automated MrBUMP searchmodel identification for map fitting in cryo-EM.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 77 (Pt 11).
pp. 1378-1385.
Abstract
In crystallography, the phase problem can often be addressed by the careful preparation of molecular-replacement search models. This has led to the development of pipelines such as MrBUMP that can automatically identify homologous proteins from an input sequence and edit them to focus on the areas that are most conserved. Many of these approaches can be applied directly to cryo-EM to help discover, prepare and correctly place models (here called cryo-EM search models) into electrostatic potential maps. This can significantly reduce the amount of manual model building that is required for structure determination. Here, MrBUMP is repurposed to fit automatically obtained PDB-derived chains and domains into cryo-EM maps. MrBUMP was successfully able to identify and place cryo-EM search models across a range of resolutions. Methods such as map segmentation are also explored as potential routes to improved performance. Map segmentation was also found to improve the effectiveness of the pipeline for higher resolution (<8 Å) data sets.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | MrBUMP, molecular replacement, cryo-EM, GroEL |
| Divisions: | Faculty of Health and Life Sciences Faculty of Health and Life Sciences > Institute of Systems, Molecular and Integrative Biology |
| Depositing User: | Symplectic Admin |
| Date Deposited: | 17 Jan 2022 10:15 |
| Last Modified: | 18 Jan 2023 21:15 |
| DOI: | 10.1107/S2059798321009165 |
| Open Access URL: | https://doi.org/10.1107/S2059798321009165 |
| Related URLs: | |
| URI: | https://livrepository.liverpool.ac.uk/id/eprint/3147006 |
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