Šimkovic, Felix
(2018)
Covariation-derived residue contacts in template-free modelling and Molecular Replacement.
Doctor of Philosophy thesis, University of Liverpool.
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Abstract
This thesis is concerned with the application of predicted residue contacts in template-free protein structure prediction and Molecular Replacement (MR). Initially, in Chapter 3, research explored the use of predicted residue contacts to improve template-free protein structure predictions, which were used to generate AMPLE ensemble search models for MR. The results proved highly encouraging: four additional targets were tractable where previous AMPLE attempts were unable to achieve structure solution. Furthermore, a novel approach to enhance b-rich decoy quality proved critical for an additional structure solution. Leading on from the work in Chapter 3, it was essential to investigate different contact prediction algorithms and ROSETTA distance-restraint energy functions to optimise decoy quality. Results presented in Chapter 4 supported previous findings, which claimed that METAPSICOV produced the most precise contact predictions. Furthermore, results showed that target-specific decoy quality may be affected by the ROSETTA distance-restraint energy function used, which also translated into MR structure solutions in AMPLE. Beyond different contact prediction algorithms and ROSETTA distance-restraint energy ... (continues)
| Item Type: | Thesis (Doctor of Philosophy) |
|---|---|
| Divisions: | Faculty of Health and Life Sciences > Institute of Systems, Molecular and Integrative Biology |
| Depositing User: | Symplectic Admin |
| Date Deposited: | 26 Mar 2019 10:12 |
| Last Modified: | 26 Oct 2024 13:41 |
| DOI: | 10.17638/03029468 |
| Supervisors: |
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| URI: | https://livrepository.liverpool.ac.uk/id/eprint/3029468 |
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