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Title: Modelling protein backbone loops using the Monte Carlo method
Author: Fernandez-Carmona, Juan
ISNI:       0000 0004 2668 9491
Awarding Body: University of Southampton
Current Institution: University of Southampton
Date of Award: 2009
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Novel methods that perform local moves such as the gaussian bias or Con- certed Rotation with Angles, increase the exploration of the conformational phase space. These methods have been applied successfully to small systems, and have proved to be more efficient than the classical Monte Carlo method. The main aim of my work was to study and include backbone moves for proteins, such as the Concerted Rotation with Angle (CRA) and the gaussian bias in the ProtoMS package. The CRA was then applied to several systems of biological interest to compute relative binding free energies and conformational changes to obtain insights into the binding mode and system flexibility. The CRA algorithm has been used to sample biological systems such as lysozyme L99A mutant, Bcr-Abl kinases and PDE5 phosphodiesterase and led to increased sampling of the backbone and more precise free energy results.
Supervisor: Essex, Jonathan Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available
Keywords: QD Chemistry