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Modelling protein backbone loops using the Monte Carlo method

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
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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More information

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
ORCID for Jonathan W. Essex: ORCID iD orcid.org/0000-0003-2639-2746

Catalogue record

Date deposited: 16 Feb 2011 15:37
Last modified: 30 Jan 2020 01:27

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Contributors

Author: Juan Fernandez-Carmona
Thesis advisor: Jonathan W. Essex ORCID iD

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