%0 Journal Article
%T β-sheet Topology Prediction Using Probability-based Integer Programming
%J Computer and Knowledge Engineering
%I Ferdowsi University of Mashhad
%Z 2538-5453
%A eghdami, mahdie
%A Dehghani, Toktam
%A Naghibzadeh, Mahmoud
%D 2018
%\ 01/01/2018
%V 1
%N 1
%P 53-64
%! β-sheet Topology Prediction Using Probability-based Integer Programming
%K β-sheet topology prediction
%K integer programming
%K Dynamic Programming
%K pairwise alignment
%R 10.22067/cke.v1i2.56005
%X β-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.
%U https://cke.um.ac.ir/article_26590_4a7c0899305f86f879f5b88b0f763f05.pdf