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3D Shape Descriptor with Interatomic Distance for Screening the Molecular Database  

Lee, Jae-Ho (동국대학교 디지털제품연구실)
Park, Joon-Young (동국대학교 산업시스템공학과)
Publication Information
Korean Journal of Computational Design and Engineering / v.14, no.6, 2009 , pp. 404-414 More about this Journal
Abstract
In the computational molecular analysis, 3D structural comparison for protein searching plays a very important role. As protein databases have been grown rapidly in size, exhaustive search methods cannot provide satisfactory performance. Because exhaustive search methods try to handle the structure of protein by using sphere set which is converted from atoms set, the similarity calculation about two sphere sets is very expensive. Instead, the filter-and-refine paradigm offers an efficient alternative to database search without compromising the accuracy of the answers. In recent, a very fast algorithm based on the inter-atomic distance has been suggested by Ballester and Richard. Since they adopted the moments of distribution with inter-atomic distance between atoms which are rotational invariant, they can eliminate the structure alignment and orientation fix process and perform the searching faster than previous methods. In this paper, we propose a new 3D shape descriptor. It has properties of the general shape distribution and useful property in screening the molecular database. We show some experimental results for the validity of our method.
Keywords
molecule database; shape descriptor; shape similarity; inter-atomic distance;
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Times Cited By KSCI : 1  (Citation Analysis)
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