**************** The 16th., Lab Seminar ****************************

Date: Thu, January 20, 2008 PM 2:30-

Place: No.616 Seminar room
　　　　　　 Graduate School of Information Science

Speaker: Takuya Okamoto

Title: Conformational States and Folding Pathways of Peptides Revealed by 
Principal-Independent Component Analysis

Phuong H. Nguyen
PROTEINS: Structure, Function, and Bioinformatics 67:579-592(2007)

Abstract:
 Principal component analysis is a powerful method for projecting 
multidimensional conformational space of peptides or proteins onto lower 
dimensional subspaces in which the main conformations are present, making 
it easier to reveal the structures of molecules from e.g. molecular 
dynamics simulation trajectories. However, the identification of all 
conformational states is still difficult if the subspaces consist of 
more than two dimensions. This is mainly due to the fact that the
principal components are not independent with each other, and states 
in the subspaces cannot be visualized. In this work, we propose a simple 
and fast scheme that allows one to obtain all conformational states in 
the subspaces. The basic idea is that instead of directly identifying 
the states in the subspace spanned by principal components, we first 
transform this subspace into another subspace formed by components that 
are independent of one other. These independent components are obtained 
from the principal components by employing the independent component 
analysis method. Because of independence between components, all states 
in this new subspace are defined as all possible combinations of the 
states obtained from each single independent component. This makes the 
conformational analysis much simpler. We test the performance of the 
method by analyzing the conformations of the glycine tripeptide and the 
alanine hexapeptide. The analyses show that our method is simple and 
quickly reveal all conformational states in the subspaces. The folding 
pathways between the identified states of the alanine hexapeptide are 
analyzed and discussed in some detail.

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