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http://dx.doi.org/10.6109/jkiice.2015.19.12.3011

Construction of Large Library of Protein Fragments Using Inter Alpha-carbon Distance and Binet-Cauchy Distance  

Chi, Sang-mun (Department of Computer Science and Engineering, Kyungsung University)
Publication Information
Journal of the Korea Institute of Information and Communication Engineering / v.19, no.12, 2015 , pp. 3011-3016 More about this Journal
Abstract
Representing protein three-dimensional structure by concatenating a sequence of protein fragments gives an efficient application in analysis, modeling, search, and prediction of protein structures. This paper investigated the effective combination of distance measures, which can exploit large protein structure database, in order to construct a protein fragment library representing native protein structures accurately. Clustering method was used to construct a protein fragment library. Initial clustering stage used inter alpha-carbon distance having low time complexity, and cluster extension stage used the combination of inter alpha-carbon distance, Binet-Cauchy distance, and root mean square deviation. Protein fragment library was constructed by leveraging large protein structure database using the proposed combination of distance measures. This library gives low root mean square deviation in the experiments representing protein structures with protein fragments.
Keywords
Protein structure; Protein fragment library; Inter alpha-carbon distance; Binet-Cauchy distance; Root mean square deviation;
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