Computer and Knowledge Engineering, Volume (1), No (1), Year (2017-2) , Pages (54-63)

Title : ( B-sheet Topology Prediction Using Probability-based Integer Programming )

Authors: Mahdie Eghdami , toktam dehghani , Mahmoud Naghibzadeh ,

Citation: BibTeX | EndNote

B-sheet topology prediction is a major unresolved problem in modern computational biology. It is a challenging intermediate step toward the protein tertiary structure prediction. Different methods have been provided to deal with the problem of determining the β-sheet topology. Here, ab-initio probability-based methods called "BetaProbe1" and "BetaProbe2" are utilized to specify the β-sheet topology. In these methods, the stability and the frequency of β-strand pairwise interaction and β-sheet conformation are spotted. To predict more frequent interactions between β-strand pairs, besides pairwise alignment probability, the probability of occurring β-strand pairwise interaction is considered to compute the score of the interactions. Furthermore, to determine the β-strand pairwise alignment probability more accurately, a dynamic programming approach is utilized. In addition, the integer programming optimization is combined with the probabilities of β-strand pairwise interactions to determine the β-sheet topology. Moreover, the β-sheet conformation probability is considered to give better chances to more observed conformations for selection. Experimental results show that BetaProbe1 and BetaProbe2 significantly outperform the most recent integer programming-based method with respect to β-sheet topology prediction

Keywords

, B, sheet topology prediction; integer programming; dynamic programming; pairwise
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@article{paperid:1061868,
author = {Eghdami, Mahdie and Dehghani, Toktam and Naghibzadeh, Mahmoud},
title = {B-sheet Topology Prediction Using Probability-based Integer Programming},
journal = {Computer and Knowledge Engineering},
year = {2017},
volume = {1},
number = {1},
month = {February},
issn = {5238-5453},
pages = {54--63},
numpages = {9},
keywords = {B-sheet topology prediction; integer programming; dynamic programming; pairwise alignment},
}

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%0 Journal Article
%T B-sheet Topology Prediction Using Probability-based Integer Programming
%A Eghdami, Mahdie
%A Dehghani, Toktam
%A Naghibzadeh, Mahmoud
%J Computer and Knowledge Engineering
%@ 5238-5453
%D 2017

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