A simple method for protein structural classification
Since the concept of structural classes of proteins was proposed, the problem of protein classification has been tackled by many groups. Most of their classification criteria are based only on the helix/strand contents of proteins. In this paper, we proposed a method for protein structural classification based on their secondary structure sequences. It is a classification scheme that can confirm existing classifications. Here a mathematical model is constructed to describe protein secondary structure sequences, in which each protein secondary structure sequence corresponds to a transition probability matrix that characterizes and differentiates protein structure numerically. Its application to a set of real data has indicated that our method can classify protein structures correctly. The final classification result is shown schematically. So it is visual to observe the structural classifications, which is different from traditional methods. (c) 2006 Elsevier Inc. All rights reserved.
structural classes secondary structure sequence transition probability matrix content of helix/strand structural characteristic vector