Binary Assignments of Amino Acids from Pattern Conservation

Details Binary Assignments of Amino Acids from Pattern Conservation Binary Assignments of Amino Acids from Pattern Conservation

1996-01-12

arxiv.org/abs/chem-ph/9601002v2

Protein Eng. 10 (1997) 1013-1017

Physics

Chemical Physics

9 pages, 4 Postscript figures. References and figure added

Scientific paper

We develop a simple optimization procedure for assigning binary values to the 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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