Extension of the pairwise-contact energy parameters for proteins with the local environments of amino acids

After parameterizing the local environments of amino acids into nine categories depending on three secondary structures and three kinds of hydrophobicity (solvation) of amino acids, we could design and construct the 16,290 pairwise-contact energy parameters of amino acids by the quasi-chemical approximation using the 937 test proteins with 30% homology, which include all representatives of the different classes of proteins. The capability of the energy parameters for recognizing the native folds of proteins is checked by the protein threading. These could recognize the 911 (97.2%) native folds of the 937 test proteins simultaneously. When these parameters are tested on the new distinct 382 proteins with 90% homology, the 372 (97.4%) proteins could recognize their native folds. Although the quasi-chemical approximation is simple, we showed that it is possible to achieve the high success ratio of recognizing the native folds of many proteins as long as all representative proteins of the different classes of proteins were considered and the local environments such as the hydrophobicity (solvation) and the secondary structures of amino acids were properly taken into account.