Computer simulations of protein folding
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 prot...
| Main Author: | |
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| Format: | Thesis (University of Nottingham only) |
| Language: | English |
| Published: |
2011
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| Online Access: | https://eprints.nottingham.ac.uk/12180/ |
| _version_ | 1848791450599292928 |
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| author | Williams, Haydn Wyn |
| author_facet | Williams, Haydn Wyn |
| author_sort | Williams, Haydn Wyn |
| building | Nottingham Research Data Repository |
| collection | Online Access |
| description | 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. |
| first_indexed | 2025-11-14T18:28:42Z |
| format | Thesis (University of Nottingham only) |
| id | nottingham-12180 |
| institution | University of Nottingham Malaysia Campus |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-14T18:28:42Z |
| publishDate | 2011 |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | nottingham-121802025-02-28T11:17:59Z https://eprints.nottingham.ac.uk/12180/ Computer simulations of protein folding Williams, Haydn Wyn 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. 2011-12-14 Thesis (University of Nottingham only) NonPeerReviewed application/pdf en arr https://eprints.nottingham.ac.uk/12180/1/thesis.pdf Williams, Haydn Wyn (2011) Computer simulations of protein folding. PhD thesis, University of Nottingham. |
| spellingShingle | Williams, Haydn Wyn Computer simulations of protein folding |
| title | Computer simulations of protein folding |
| title_full | Computer simulations of protein folding |
| title_fullStr | Computer simulations of protein folding |
| title_full_unstemmed | Computer simulations of protein folding |
| title_short | Computer simulations of protein folding |
| title_sort | computer simulations of protein folding |
| url | https://eprints.nottingham.ac.uk/12180/ |