Novel protein weight matrix generated from amino acid indices

In recent years, numerous protein weight matrices have been developed that include physical characteristics of proteins, such as local sequence-structure information, alpha-helix information, secondary structure information and solvent accessibility states. These protein weight matrices are shown to have generally improved protein sequence alignments over classical protein weight matrices, like Point Accepted Mutation (PAM), Blocks of Amino Acid Substitution (BLOSUM), and GONNET matrices, where important limitations have been observe in recent works. In this paper, a novel protein weight matrix is constructed and presented. This protein weight matrix is not considered based on the mutation rate, like PAM or BLOSUM matrices, but on the physicochemical properties of each amino acid. In the literature, over 500 amino acid indices exist, each one representing a unique biological protein feature. For this study, 25 amino acid indices were selected. These amino acid indices represent general and widely accepted features of the amino acids. By using the proposed protein weight matrix the following advantages can be obtained compared to the classical protein weight matrices. The proposed protein weight matrix is not biased to specific groups of protein sequences as the values are calculated from the amino acid indices, and not from the protein sequences. Additionally, for the proposed protein weight matrix, the same matrix can be considered regardless of the protein sequence's homology to be aligned or the mutation rate presented. A correlation to the physical characterisations of the amino acids that the protein weight matrix derived from can be achieved. Different similarity matrices can be generated when different physical characterisations of amino acids are considered.