A Demonstration of Clustering in Protein Contact Maps for Alpha Helix Pairs

Abstract. The purpose of this work is to demonstrate that it is possible to cluster contact maps for pairs of alpha helices such that each of the clusters corresponds to a group of pairs of alpha helices with similar properties. The property of the configuration of helix pairs that was chosen for study is the packing attribute. The contact maps are compared to one another using a novel contact map comparison scheme based upon the locations of contacts in the contact maps. A k-nearest neighbours technique is used to perform the clustering, and the cosine between vectors corresponding to contact map regions was the distance metric. The clustering of contact maps to determine whether maps corresponding to similar packing values are placed into the same clusters yielded promising results.

• Type: Conference
• Year: 2007
• Where: ICANNGA
• Authors: Robert Fraser, Janice I. Glasgow
• Keywords: Alpha Helices, Contact Maps, Helix Pairs, ICANNGA 2007