Designing potential energy functions for protein folding

Current Opinion in Structural Biology

Volumn 9, Issue 2, 1999, Pages 184-188

  Hao, Ming Hong ^a,b   Scheraga, Harold A ^b  

^a BIP Inc   (United States)

^b Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ALGORITHM; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN FOLDING; REVIEW; THERMODYNAMICS;

EID: 0033117762     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(99)80026-8     Document Type: Article

References (40)

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20. Koretke KK, Luthey-Schulten Z, Wolynes PG: Self-consistently optimized energy functions for protein structure prediction by molecular dynamics. Proc Natl Acad Sci USA 1998, 95:2932-2937. In this paper, a general strategy is proposed for optimizing the energy parameters of a potential function by taking into account both the major determinant and the secondary contributions. The methods for sampling the misfolded conformations of protein models and the approach for treating the heterogeneity of different proteins in the optimization are also provided. Tests of the method on an ensemble of eight proteins are described and reasonably good results for folding are reported.
21. Chiu TL, Goldstein RA: Optimizing energy potentials for success in protein tertiary structure prediction. Fold Des 1998, 3:223-228. An alternative procedure is proposed for optimizing a potential energy function for an ensemble of proteins. The average success of folding all the proteins in the training set is maximized in this approach.
22. Kolinski A, Galazka W, Skolnick J: Monte Carlo studies of the thermodynamics and kinetics of reduced protein models. Application to small helical, beta and alpha-beta proteins. J Chem Phys 1998, 108:2608-2617. This paper is one of a series of publications from the same group, in which a general strategy for deriving a potential energy function for the folding of more realistic models of proteins is developed.
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31. Chung MS, Neuwald AF, Wilbur WJ: A free energy analysis by unfolding applied to 125-mers on a cubic lattice. Fold Des 1998, 3:51-65. A method is proposed for calculating the free-energy profile of protein models based on restricted Monte Carlo simulations and conformational sampling over a restricted conformational window. The calculated free-energy profile is used to characterize the foldability of protein models. The method was tested on cubic-lattice proteins with 27-mer and 125-mer chain lengths.
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35. •] than to the simple cubic- lattice protein models.
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39. Liwo A, Kazmierkiewicz R, Czaplewski C, Groth M, Oldziej S, Wawak RJ, Rackovsky S, Pincus MR, Scheraga HA: United-residue force field for off-lattice protein-structure simulations; III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials. J Comput Chem 1998, 19:259-276.
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