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International Journal of Information Technology & Computer Science ( IJITCS )

Abstract :

Proteins have a flexible structure and undergo structural rearrangements during their activities. However, most of the protein structure alignment methods consider them as rigid bodies. In this paper, we report a linear encoding based method for flexible alignment of protein structure. In the first step, the method looks for Aligned Fragment Pairs (AFP) between two proteins, and then, uses a text modeling technique to create a topology string for each AFP. The generated topology strings of two proteins are compared and aligned using n-gram modeling technique over entropy concept. Finally, a step-by-step algorithm is utilized to create alignment between two structures. The method was evaluated by a set of experiments using a dataset of proteins with macromolecular motions and the results were compared with those of the existing flexible alignment methods e.g. FlexProt, FATCAT, and FlexSnap. The results prove the efficiency and applicability of the proposed method in comparison with the other similar methods .

Keywords :

: protein structure alignment; flexible alignment; structure comparison

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