New scoring matrix for amino acid residue exchanges based on residue characteristic physical parameters

Based on residue characteristic physical parameters, a new scoring matrix, called EMPAR, for amino acid exchanges in proteins was obtained. When comparing protein sequences for detecting homologies, the use of this matrix in place of the Dayhoff log-odds matrix yields results that reflect the topological similarities in the proteins. The use of EMPAR is equivalent to the parametric correlates coefficient approach of Ooi and his colleagues. This matrix correlates at 0.63 with the Dayhoff matrix.