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Design of an optimal Chebyshev‐expanded discrimination function for globular proteins
Author(s) -
Fain Boris,
Xia Yu,
Levitt Michael
Publication year - 2002
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.0200702
Subject(s) - decoy , globular protein , chebyshev filter , representation (politics) , function (biology) , histogram , algorithm , chebyshev polynomials , mathematics , computer science , mathematical analysis , physics , artificial intelligence , chemistry , image (mathematics) , nuclear magnetic resonance , biochemistry , receptor , evolutionary biology , politics , political science , law , biology
We describe the construction of a scoring function designed to model the free energy of protein folding. An optimization technique is used to determine the best functional forms of the hydrophobic, residue‐residue and hydrogen‐bonding components of the potential. The scoring function is expanded by use of Chebyshev polynomials, the coefficients of which are determined by minimizing the score, in units of standard deviation, of native structures in the ensembles of alternate decoy conformations. The derived effective potential is then tested on decoy sets used conventionally in such studies. Using our scoring function, we achieve a high level of discrimination between correct and incorrect folds. In addition, our method is able to represent functions of arbitrary shape with fewer parameters than the usual histogram potentials of similar resolution. Finally, our representation can be combined easily with many optimization methods, because the total energy is a linear function of the parameters. Our results show that the techniques of Z‐score optimization and Chebyshev expansion work well.