Amino acid classes and the protein folding problem
Marek Cieplak, Neal S. Holter, Amos Maritan, Jayanth R. Banavar
Abstract
We present and implement a distance-based clustering of amino acids within the framework of a statistically derived interaction matrix and show that the resulting groups faithfully reproduce, for well-designed sequences, thermodynamic stability in and kinetic accessibility to the native state. A simple interpretation of the groups is obtained by eigenanalysis of the interaction matrix.
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