Title
Discovery of spatially cohesive itemsets in three-dimensional protein structures Discovery of spatially cohesive itemsets in three-dimensional protein structures
Author
Faculty/Department
Faculty of Sciences. Mathematics and Computer Science
Publication type
article
Publication
New York, N.Y. ,
Subject
Mathematics
Chemistry
Biology
Computer. Automation
Source (journal)
IEEE/ACM transactions on computational biology and bioinformatics / Institute of Electrical and Electronics Engineers [New York, N.Y.] - New York, N.Y.
Volume/pages
11(2014) :5 , p. 814-825
ISSN
1545-5963
ISI
000346629600005
Carrier
E
Target language
English (eng)
Full text (Publishers DOI)
Affiliation
University of Antwerp
Abstract
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.
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