Name
Title | ||
|---|---|---|
Determination of optimal Chebyshev-expanded hydrophobic discrimination function for globular proteins |
Abstract | ||
|---|---|---|
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. |
Year | DOI | Venue |
|---|---|---|
2001 | 10.1147/rd.453.0525 | IBM Journal of Research and Development |
Keywords | Field | DocType |
alternate conformation,chebyshev polynomial,optimization technique,z-score optimization,protein folding,chebyshev expansion work,hydrophobic potential,hydrophobic effect,optimal chebyshev-expanded hydrophobic discrimination,scoring function,effective potential,globular protein,discriminant function | Chebyshev polynomials,Discrimination function,Protein folding,Combinatorics,Biological system,Decoy,Globular protein,Electronic engineering,Chebyshev filter,Hydrophobic effect,Standard deviation,Mathematics | Journal |
Volume | Issue | ISSN |
45 | 3-4 | 0018-8646 |
Citations | PageRank | References |
0 | 0.34 | 0 |
Authors | ||
3 | ||