Mahdi Eghdami - Department of Computer Engineering, Engineering Faculty, Ferdowsi University of Mashhad, Mashhad, Iran
Toktam Dehghani - Department of Computer Engineering, Engineering Faculty, Ferdowsi University of Mashhad, Mashhad, Iran
Mahmoud Naghibzadeh - Department of Computer Engineering, Engineering Faculty, Ferdowsi University of Mashhad, Mashhad, Iran

β-sheet topology prediction is a major unresolved problem in modern computational biology. It is a challenging inermediate 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 Beta Probel 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 occuring 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 probabilites 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 BetaProbel and BetaProbe2 significantly outperform the most recent integer programming-based method with respect to β-sheet topology prediction.

β-sheet topology prediction, integer programming, dynamic programming, pairwise alignment