Evolution of Amino Acid Properties in the Context of Protein Secondary Structure Prediction

Amino acid properties were optimized for protein secondary structure prediction. The artificial properties were evolved using differential evolution in a property space of arbitrary dimensionality. These properties were optimized to provide the correct results in predicting the elements of the protein secondary structure using a simple classifier model and with standard benchmark sets. A comparison is performed with respect to the use of the commonly employed orthogonal and neutral encoding of the amino acids of the protein chain, together with a discussion of the similarities of the evolved artificial properties with respect to physical properties of amino acids.