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Article
Minimization of empirical energy functions in proteins including hydrophobic surface area effects
Article first published online: 7 SEP 2004
DOI: 10.1002/jcc.540140503
Copyright © 1993 John Wiley & Sons, Inc.
1096-987X/asset/cover.gif?v=1&s=4429aac2462ebd499c13b3d7fe983679c5767778 "Journal of Computational Chemistry")
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How to Cite
Freyberg, B. V. and Braun, W. (1993), Minimization of empirical energy functions in proteins including hydrophobic surface area effects. J. Comput. Chem., 14: 510–521. doi: 10.1002/jcc.540140503
Publication History
- Issue published online: 7 SEP 2004
- Article first published online: 7 SEP 2004
- Manuscript Accepted: 12 OCT 1992
- Manuscript Received: 22 JUL 1992
- Abstract
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Abstract
We present analytical expressions to calculate the gradient of the water-accessible surface area of proteins with respect to Cartesian coordinates and dihedral angles. A detailed mathematical analysis leads to corrected equations for the gradient calculation used previously in the ANAREA program. To study the hydrophobic effect of solvent-protein interactions, our expressions have been implemented to further improve the program package FANTOM. We used this version of FANTOM to minimize the ECEPP/2 and the hydrophobic energy of tendamistat. © 1993 John Wiley & Sons, Inc.