ABSTRACT We consider the problem of ¯nding over-represented arrange- ments of Secondary Structure Elements (SSEs) in a given dataset of representative protein structures. While most pa- pers in the literature study the distribution of geometrical properties, in particular angles and distances, between pairs of interacting SSEs, in this paper we focus on the distribu- tion of angles of all quartets of SSEs and on the extraction of over-represented angular patterns. We propose a variant of the Apriori method that obtains over-represented arrange- ments of quartets of SSEs by combining arrangements of triplets of SSEs. This speci¯c case will pose the basis for a natural extension of the problem to any given number of SSEs. We analyze the results of our method on a dataset of 300 non redundant proteins.
Mining Over-Represented 3D Patterns of Secondary Structures in Proteins
COMIN, MATTEO;GUERRA, CONCETTINA;G, ZANOTTI
2007
Abstract
ABSTRACT We consider the problem of ¯nding over-represented arrange- ments of Secondary Structure Elements (SSEs) in a given dataset of representative protein structures. While most pa- pers in the literature study the distribution of geometrical properties, in particular angles and distances, between pairs of interacting SSEs, in this paper we focus on the distribu- tion of angles of all quartets of SSEs and on the extraction of over-represented angular patterns. We propose a variant of the Apriori method that obtains over-represented arrange- ments of quartets of SSEs by combining arrangements of triplets of SSEs. This speci¯c case will pose the basis for a natural extension of the problem to any given number of SSEs. We analyze the results of our method on a dataset of 300 non redundant proteins.Pubblicazioni consigliate
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