Tools and algorithms for refined comparison of protein structures

Authors:
Yaw-Ling Lin;Shih-Peng Huang
Affiliations:
Providence University, Dept. Comput. Sci. & Info. Engineering, Taichung, Taiwan;Providence University, Dept. Comput. Sci. & Info. Management, Taichung, Taiwan
Venue:
MINO'07 Proceedings of the 6th conference on Microelectronics, nanoelectronics, optoelectronics
Year:
2007

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Abstract

Protein structure provides the opportunity to recognize homology that is undetectable by sequence comparison, and it represents a powerful means of discovering functions, yielding direct insight into the molecular mechanisms. In this paper, we propose algorithms and develop tools for pairwise alignment of protein structures. Methods of locating suitable isometric transformations of one structure and aligning it to the other structure are addressed. Our methods allow sequence gaps of any length, reversal of chain direction, and free topological connectivity of atom sequences. We show the effectiveness of the proposed refinement methods by a set of experiments, which improve several previous results.