Bulletin of the Korean Chemical Society

  • 제31권5호
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  • Pages.1247-1251
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  • 2010
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  • 0253-2964(pISSN)
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  • 1229-5949(eISSN)
대한화학회 (Korean Chemical Society)
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Computational Prediction of Solvation Free Energies of Amino Acids with Genetic Algorithm

  • Park, Jung-Hum (Department of Bioscience and Biotechnology, Sejong University) ;
  • Lee, Jin-Won (Department of Life Science, Hanyang University) ;
  • Park, Hwang-Seo (Department of Bioscience and Biotechnology, Sejong University)
  • 투고 : 2010.02.17
  • 심사 : 2010.03.05
  • 발행 : 2010.05.20
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초록

We propose an improved solvent contact model to estimate the solvation free energies of amino acids from individual atomic contributions. The modification of the solvation model involves the optimization of three kinds of parameters in the solvation free energy function: atomic fragmental volume, maximum atomic occupancy, and atomic solvation parameters. All of these atomic parameters for 17 atom types are developed by the operation of a standard genetic algorithm in such a way to minimize the difference between experimental and calculated solvation free energies. The present solvation model is able to predict the experimental solvation free energies of amino acids with the squared correlation coefficients of 0.94 and 0.93 for the parameterization with Gaussian and screened Coulomb potential as the envelope functions, respectively. This result indicates that the improved solvent contact model with the newly developed atomic parameters would be a useful tool for the estimation of the molecular solvation free energy of a protein in aqueous solution.

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피인용 문헌

  1. Comprehensive Studies on the Free Energies of Solvation and Conformers of Glycine: A Theoretical Study vol.32, pp.6, 2011, https://doi.org/10.5012/bkcs.2011.32.6.1985
  2. Structural and vibrational study on zwitterions of l-threonine in aqueous phase using the FT-Raman and SCRF calculations vol.1045, pp.None, 2010, https://doi.org/10.1016/j.molstruc.2013.04.016