Mining overrepresented 3D patterns of secondary structures in proteins.
We consider the problem of finding overrepresented arrangements of secondary structure elements (SSEs) in a given dataset of representative protein structures. While most papers 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 distribution of angles of all quartets of SSEs and on the extraction of overrepresented angular patterns. We propose a variant of the Apriori method that obtains overrepresented arrangements of quartets of SSEs by combining arrangements of triplets of SSEs. This specific 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 nonredundant proteins. Supplementary material is available at (http://www.dei.unipd.it/nciompin/papers/CGZ-jbcb-suppl.pdf/).
Comin
Matteo
M
Department of Information Engineering, University of Padova, Padova, Italy. ciompin@dei.unipd.it
Guerra
Concettina
C
Zanotti
Giuseppe
G
D000465:Algorithms; D019295:Computational Biology; D030562:Databases, Protein / Q000706:statistics & numerical data*; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
D011506:Proteins