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A Multisequence Monte Carlo Method in a Simple Protein Model

Nilsson, Daniel LU (2014) FYTK01 20141
Computational Biology and Biological Physics - Has been reorganised
Abstract
In this thesis an algorithm for simulating the equilibrium behavior of a large number of protein sequences at fixed temperature in a single run is investigated. The method, which works by allowing Monte Carlo updates of the protein sequence, is implemented and tested for a simple reduced-representation continuous protein model with three different types of amino acids.

The effectiveness of the model is related to that of a naive fixed-sequence Monte Carlo algorithm, by comparing thermalization times and statistical errors. The new algorithm is found to have considerably shorter thermalization times, and statistical errors of similar or lower magnitude for most sequences investigated.

Finally, the method is used to investigate the... (More)
In this thesis an algorithm for simulating the equilibrium behavior of a large number of protein sequences at fixed temperature in a single run is investigated. The method, which works by allowing Monte Carlo updates of the protein sequence, is implemented and tested for a simple reduced-representation continuous protein model with three different types of amino acids.

The effectiveness of the model is related to that of a naive fixed-sequence Monte Carlo algorithm, by comparing thermalization times and statistical errors. The new algorithm is found to have considerably shorter thermalization times, and statistical errors of similar or lower magnitude for most sequences investigated.

Finally, the method is used to investigate the sequence-structure relationship for short model proteins with eight amino acids. Sequences folding to certain structures were mapped, and the number of sequences folding to each were determined, as well as the number of mutational transitions between them. (Less)
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author
Nilsson, Daniel LU
supervisor
organization
course
FYTK01 20141
year
type
M2 - Bachelor Degree
subject
keywords
Proteins, Monte Carlo, Multisequence, Evolution
language
English
id
4466164
date added to LUP
2014-06-17 07:55:06
date last changed
2017-10-06 16:30:31
@misc{4466164,
  abstract     = {{In this thesis an algorithm for simulating the equilibrium behavior of a large number of protein sequences at fixed temperature in a single run is investigated. The method, which works by allowing Monte Carlo updates of the protein sequence, is implemented and tested for a simple reduced-representation continuous protein model with three different types of amino acids. 

The effectiveness of the model is related to that of a naive fixed-sequence Monte Carlo algorithm, by comparing thermalization times and statistical errors. The new algorithm is found to have considerably shorter thermalization times, and statistical errors of similar or lower magnitude for most sequences investigated. 

Finally, the method is used to investigate the sequence-structure relationship for short model proteins with eight amino acids. Sequences folding to certain structures were mapped, and the number of sequences folding to each were determined, as well as the number of mutational transitions between them.}},
  author       = {{Nilsson, Daniel}},
  language     = {{eng}},
  note         = {{Student Paper}},
  title        = {{A Multisequence Monte Carlo Method in a Simple Protein Model}},
  year         = {{2014}},
}