Mining spatially cohesive itemsets in protein molecular structures

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. The usefulness of this algorithm 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. The experiments show that several patterns found by the cohesive structural itemset miner contain amino acids that frequently co-occur inthe 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.

Publication year:2013

Keywords:Biology

Accessibility:Closed