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Discovery of Spatially Cohesive Itemsets in Three-dimensional Protein Structures
PrePrint
ISSN: 1545-5963
Cheng Zhou, Cheng Zhou is with the Department of Mathematics and Computer Science, University of Antwerp, Belgium.(email:cheng.zhou@uantwerpen.be)
In this paper we present a cohesive structural itemset miner aiming to discover interesting patterns in a set of data objects within a multidimensional spatial structure by combining the cohesion and the support of the pattern. We propose two ways to build the itemset miner, VertexOne and VertexAll, in an attempt to find a balance between accuracy and run-times. The experiments show that VertexOne performs better, and finds almost the same itemsets as VertexAll in a much shorter time. The usefulness of the method is demonstrated by applying it to find interesting patterns of amino acids in spatial proximity within a set of proteins based on their atomic coordinates in the protein molecular structure. Several patterns found by the cohesive structural itemset miner contain amino acids that frequently co-occur in the spatial structure, even if they are distant in the primary protein sequence and only brought together by protein folding. Further various indications were found that some of the discovered patterns seem to represent common underlying support structures within the proteins.
Index Terms:
Itemsets,Proteins,Amino acids,Data mining,Protein engineering,Bioinformatics,IEEE transactions
Citation:
Boris Cule, Kris Laukens, Bart Goethals, Cheng Zhou, Pieter Meysman, "Discovery of Spatially Cohesive Itemsets in Three-dimensional Protein Structures," IEEE/ACM Transactions on Computational Biology and Bioinformatics, 24 March 2014. IEEE computer Society Digital Library. IEEE Computer Society, <http://doi.ieeecomputersociety.org/10.1109/TCBB.2014.2311795>
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