Numerical recipes in C (2nd ed.): the art of scientific computing
Numerical recipes in C (2nd ed.): the art of scientific computing
Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications
Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications
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We describe the development of a scoring function designed to model the hydrophobic effect in protein folding. An optimization technique is used to determine the best functional form of the hydrophobic potential. The scoring function is expanded using the Chebyshev polynomials, for which the coefficients are determined by minimizing the Z-score of native structures in the ensembles of alternate conformations. (The Z-score is the score relative to the mean, measured in units of standard deviation.) The derived effective potential is tested on decoy sets conventionally used in such studies. The function is able to discriminate very well between correct and incorrect folds, despite the fact that it simply counts the number of neighbors of each amino acid. Our results show that the techniques of Z-score optimization and Chebyshev expansion work, and work well. Our results also confirm that hydrophobic effect is one of the principal driving forces in protein folding.