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|Title: ||Multiple Structure Alignment Based on Geometrical Correlation of Secondary Structure Elements|
|Authors: ||TUN-WEN PAI;RUEI-HSIANG CHANG;CHIEN-MING CHEN;PO-HAN SU;LEE-JYI WANG;KUEN-TSAIR LAY;KUO-TORNG LAN|
|Contributors: ||NTOU:Department of Computer Science and Engineering|
|Keywords: ||Multiple structure alignment;secondary structure;angle distance map;geometrical correlation|
|Issue Date: ||2011-10-21T02:34:14Z
|Publisher: ||New Mathematics and Natural Computation Journal|
|Abstract: ||Abstract:Protein structure alignment facilitates the analysis of protein functionality. Through superimposed structures and the comparison of variant components, common or speci¯c features of proteins can be identi¯ed. Several known protein families exhibit analogous tertiary structures but divergent primary sequences. These proteins in the same structural class are unable to be aligned by sequence-based methods. The main objective of the present study was to develop an e±cient and eRective algorithm for multiple structure alignment based on geometrical correlation of secondary structures, which are conserved in evolutionary heritage. The method utilizes mutual correlation analysis of secondary structure elements (SSEs) and selects representative segments as the key anchors for structural alignment. The system exploits a fast vector transformation technique to represent SSEs in vector format, and the mutual geometrical relationship among vectors is projected onto an angle-distance map. Through a scoring function and fltering mechanisms, the best candidates of vectors are selected, and an eRective constrained multiple structural alignment module is performed. The correctness of the algorithm was veri¯ed by the multiple structure alignment of proteins in the SCOP database. Several protein sets with low sequence identities were aligned, and the results were compared with those obtained by three well-known structural alignment approaches. The results show that the proposed method is able to perform multiple structural alignments eRectively and to obtain satisfactory results, especially for proteins possessing low sequence identity.|
|Relation: ||6(1), pp.77-95|
|Appears in Collections:||[資訊工程學系] 期刊論文|
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