Representing Inter-residue Dependencies in Protein Sequences with Probabilistic Networks

Hiroshi Mamitsuka (mami@sbl.cl.nec.co.jp)

C&C Research Labs., NEC Corporation
1-1, Miyazaki 4-chome, Miyamae-ku, Kawasaki, Kanagawa 216, Japan

We propose a new method for representing a local region of a protein sequence as a probabilistic network. The method produces, from a large number of examples of a local region, a network which describes dependency relationships that exist among amino acid residues in the region. The network is constructed using the greedy-search algorithm based on the minimum description length (MDL) principle. In our experiments, we construct two probabilistic networks of two alpha-helix regions in globin family protein. Experimental results show that our method provides a visual aid to understanding inter-residue dependencies of those regions with probabilistic networks, and the networks capture several important features which are peculiar to those regions.