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Mihail, A. (2017) Visualising protein unfolding pathways. Göteborg : Chalmers University of Technology
BibTeX
@mastersthesis{
Mihail2017,
author={Mihail, Anton},
title={Visualising protein unfolding pathways},
abstract={Observing interactive unfolding animations of proteins improves the understanding
of protein chain movements. This work focuses on how the movements can be computed
using a reduced conformational space, made of mesostates. To this end, the
present work has implemented through constructive research an extension of a popular
molecular visualisation software. The extension uses beam search to generate
a motion graph from which an unfolding pathway is extracted with a shortest-path
algorithm. The unfolding animation is obtained by morphing the protein chain
through the pathway’s conformations. The results for unfolding ubiquitin resemble,
to some extent, the reverse of the folding through molecular dynamics. Results also
show that different parameters are needed for unfolding a knotted protein and -
sheet rich proteins. The extension shows that the protein main chain movements can
be restricted to mesostates. The extension also proved to be helpful in discussing
unfolding functions and provides a platform for verifying such functions.},
publisher={Institutionen för data- och informationsteknik (Chalmers), Chalmers tekniska högskola},
place={Göteborg},
year={2017},
keywords={protein, unfolding, pathway, visualisation, animation, motion planning, beam search, mesostates},
note={59},
}
RefWorks
RT Generic
SR Electronic
ID 250603
A1 Mihail, Anton
T1 Visualising protein unfolding pathways
YR 2017
AB Observing interactive unfolding animations of proteins improves the understanding
of protein chain movements. This work focuses on how the movements can be computed
using a reduced conformational space, made of mesostates. To this end, the
present work has implemented through constructive research an extension of a popular
molecular visualisation software. The extension uses beam search to generate
a motion graph from which an unfolding pathway is extracted with a shortest-path
algorithm. The unfolding animation is obtained by morphing the protein chain
through the pathway’s conformations. The results for unfolding ubiquitin resemble,
to some extent, the reverse of the folding through molecular dynamics. Results also
show that different parameters are needed for unfolding a knotted protein and -
sheet rich proteins. The extension shows that the protein main chain movements can
be restricted to mesostates. The extension also proved to be helpful in discussing
unfolding functions and provides a platform for verifying such functions.
PB Institutionen för data- och informationsteknik (Chalmers), Chalmers tekniska högskola,
LA eng
LK http://publications.lib.chalmers.se/records/fulltext/250603/250603.pdf
OL 30
