This paper introduces a novel method for theoretical determination of amino acid substitution groups. The method here involves making a binary matrix based on 48 qualitative physicochemical properties and calculating a substitution matrix based on this using dot products. Isolated groups with high scores are determined to be valid substitution groups and conserved groups are derived from these ...

We have used analysis of variance to partition the variation in synonymous and amino acid substitution rates between three effects (gene, lineage, and a gene-by-lineage interaction) in mammalian nuclear and mitochondrial genes. We find that gene effects are stronger for amino acid substitution rates than for synonymous substitution rates and that lineage effects are stronger for synonymous subs...

amino acid dehydrogenases (l-amino acid: oxidoreductase deaminating ec 1.4.1.x) are members of the wider superfamily of oxidoreductases that catalyze the reversible oxidative deamination of an amino acid to its keto acid and ammonia with the concomitant reduction of either nad+, nadp+ or fad. these enzymes have been received much attention as biocatalysts for use in biosensors or diagnostic kit...

Models of amino acid substitution were developed and compared using maximum likelihood. Two kinds of models are considered. "Empirical" models do not explicitly consider factors that shape protein evolution, but attempt to summarize the substitution pattern from large quantities of real data. "Mechanistic" models are formulated at the codon level and separate mutational biases at the nucleotide...

objectives analysis of ns5a polymorphisms in hcv genotype 1b pre-treatment serum samples from estonian patients and their effect on the treatment response. patients and methods twenty-nine complete ns5a sequences obtained from patients with chronic hcv-1b infection who had received combined therapy with pegifnα-2a/rbv were analyzed and compared with the prototype strain hcv-j. twelve patients a...