Simpkin, Adam 
ORCID: 0000-0003-1883-9376
(2020)
Exploring unconventional approaches to Molecular Replacement in X-ray crystallography with SIMBAD.
PhD thesis, University of Liverpool.
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Abstract
Molecular replacement (MR) is the most popular technique to solve the phase problem in macromolecular crystallography. The conventional approach to finding search models for MR is to use the sequence of the target structure to identify a suitable homologue. This approach is based on the assumption that sequence similarity is a useful guide to structural similarity. Whilst largely true, this strategy is not always effective. For example, when a contaminant protein has been crystallised or when the most similar matches sequentially are not the most similar structurally. This thesis describes the development of SIMBAD, a three-step pipeline to perform sequence-independent MR. The first step performs a lattice-parameter search against the entire Protein Data Bank (PDB), rapidly determining whether the protein or a close homologue has been solved in the same crystal form. The second step is designed to screen the data against a database of known contaminants; thus determining if a contaminant protein has been crystallised. The final step is a brute-force search of a non-redundant derivative of the PDB provided by the MoRDa software package. In Chapter 3 the initial implementation of SIMBAD using AMoRe’s fast ... (continues)
| Item Type: | Thesis (PhD) |
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| Divisions: | Faculty of Health and Life Sciences > Institute of Systems, Molecular and Integrative Biology |
| Depositing User: | Symplectic Admin |
| Date Deposited: | 08 Apr 2020 14:23 |
| Last Modified: | 08 Feb 2025 02:04 |
| DOI: | 10.17638/03072448 |
| Supervisors: |
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| URI: | https://livrepository.liverpool.ac.uk/id/eprint/3072448 |
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