Hybrid Protein Model: a new clustering approach for 3D local structures: Evolution of Hybrid Protein ModelReport as inadecuate




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* Corresponding author 1 Modélisation mathématique et statistique en biologie et médecine

Abstract : The -Hybrid Protein Model- HPM is a fuzzy model for compacting biological data series such as 3D structures into a limited number of overlapping cluster. The 3D structures of a non-redundant structural databank is encoded in a previously defined structural alphabet composed of 16 protein blocks PBs 1. The hybrid protein is composed of a series of distributions of the probability of observing the PBs. The training is an iterative unsupervised process that for every fold to be learn consists of looking for the most similar pattern present in the hybrid protein and modifying it slightly. Finally each position of the hybrid protein corresponds to a set of similar local structures. Compared with conventional clustering and the definition of a partition into independent subsets, the hybrid protein characterizes a series of structurally dependent subsets: that is, it maintains the sequentiality of the local structures. In a second step, to define the optimal length of the hybrid protein, we have defined an new approach based on the deletion of the redundant parts of the hybrid protein.

Keywords : fold library protein block unsupervisied classifier 3D protein structure clustering





Author: Cristina Benros - Serge Hazout - Alexandre De Brevern -

Source: https://hal.archives-ouvertes.fr/



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