Binary assignments of amino acids from pattern conservation

• We have developed a simple optimization procedure for assigning binary values to amino acids. The binary values are determined by a maximization of the degree of pattern conservation in groups of closely related protein sequences. The maximization is carried out at fixed composition. For compositions approximately corresponding to an equipartition of the residues, the optimal encoding is found to be strongly correlated with hydrophobicity. The stability of the procedure is demonstrated. Our calculations are based upon sequences in the SWISS-PROT database.

Nyckelord

Amino Acids

Databases, Factual

Fourier Analysis

Models, Chemical

Peptide Mapping

Protein Folding

Proteins

Publikations- och innehållstyp

art (ämneskategori)

ref (ämneskategori)