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Finding Optimal Structural Motif in Protein Structures by Network Alignment

Lu-Lu Chang

Abstract



Structural Motif finding in protein structures is one of the major goals of functional genomics. So far, various computational methods have been proposed for alignment or comparison of proteins using sequence or structure information. In this paper, the idea of network alignment is introduced to this never ending story. We proposed a motif finding method by combing the sequence information in node similarity with structure information in edge similarity in network alignment framework as an optimization problem. After proper modeling the 3D structural motif finding problem is formed into a linear programming problem and LP-based algorithm is designed. Preliminary results demonstrate the effectiveness of the proposed approach.

Keywords


3D structural motif, protein structure network, network alignment.

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