Computer simulations of protein folding

Williams, Haydn Wyn (2011) Computer simulations of protein folding. PhD thesis, University of Nottingham.

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Abstract

Computer simulations of biological systems provide novel data while both supporting and challenging traditional experimental methods. However, continued innovation is required to ensure that these technologies are able to work with increasingly complex systems.

Coarse–grained approximations of protein structure have been studied using a lattice model designed to find low–energy conformations. A hydrogen–bonding term has been introduced. The ability to form β–sheet has been demonstrated, and the intricacies of reproducing the more complex α–helix on a lattice have been considered.

An alternative strategy, that of better utilising computing power through the technique of milestoning, has shown good agreement with previous experimental and computational work. The increased efficiency allows significantly less extreme simulation conditions to be applied than those used in alternative simulation methods, and allows more simulation repeats.

Finally, the principles of Least Action Dynamics have been employed to combine the two approaches described above. By splitting a simulation trajectory into a number of smaller components, and using the lattice model to optimise the path from a start structure to an end structure, it has been possible to efficiently generate dynamical information using an alternative method to traditional molecular dynamics.

Item Type: Thesis (University of Nottingham only) (PhD)
Supervisors: Williams, P.M.
Hirst, J.D.
Subjects: Q Science > QA Mathematics > QA 75 Electronic computers. Computer science
Q Science > QP Physiology > QP501 Animal biochemistry
Faculties/Schools: UK Campuses > Faculty of Science > School of Pharmacy
Item ID: 12180
Depositing User: EP, Services
Date Deposited: 06 Mar 2012 10:28
Last Modified: 17 Sep 2016 21:53
URI: http://eprints.nottingham.ac.uk/id/eprint/12180

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