Modelling protein backbone loops using the Monte Carlo method
Modelling protein backbone loops using the Monte Carlo method
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.
Fernandez-Carmona, Juan
05439cd0-f2c0-4283-9a99-8edd94977a21
3 April 2009
Fernandez-Carmona, Juan
05439cd0-f2c0-4283-9a99-8edd94977a21
Essex, Jonathan W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5
Fernandez-Carmona, Juan
(2009)
Modelling protein backbone loops using the Monte Carlo method.
University of Southampton, School of Chemistry, Doctoral Thesis, 165pp.
Record type:
Thesis
(Doctoral)
Abstract
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.
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Published date: 3 April 2009
Organisations:
University of Southampton
Identifiers
Local EPrints ID: 173851
URI: http://eprints.soton.ac.uk/id/eprint/173851
PURE UUID: 31b02a22-faf6-4d8f-9288-7959c9b8f896
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Date deposited: 16 Feb 2011 15:37
Last modified: 14 Mar 2024 02:37
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Author:
Juan Fernandez-Carmona
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