Binary assignments of amino acids from pattern conservation

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Abstract

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.

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Keywords

  • Amino Acids, Databases, Factual, Fourier Analysis, Models, Chemical, Peptide Mapping, Protein Folding, Proteins
Original languageEnglish
Pages (from-to)1013-7
Number of pages5
JournalProtein Engineering
Volume10
Issue number9
Publication statusPublished - 1997 Sep
Publication categoryResearch
Peer-reviewedYes