Pairwise calculation of protein solvent-accessible surface areas

Folding and Design

Volumn 3, Issue 4, 1998, Pages 253-258

  Street, Arthur G ^a   Mayo, Stephen L ^a  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Dead end elimination; Hydrophobic burial; Pairwise surface area; Protein design; Solvent accessible surface area

Indexed keywords

SOLVENT;

ALGORITHM; ARTICLE; COVALENT BOND; HYDROPHOBICITY; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN STABILITY;

EID: 0031844416     PISSN: 13590278     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1359-0278(98)00036-4     Document Type: Article

References (14)

1. Desmet, J., De Maeyer, M., Hazes, B. & Lasters, I. (1992). The deadend elimination theorem and its use in protein sidechain positioning. Nature 356, 539-542.
2. Lee, B. & Richards, P.M. (1971). The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55, 379-400.
3. Wodak, S.J. & Janin, J. (1980). Analytical approximation to the accessible surface area of proteins. Proc. Natl Acad. Sci. USA 77, 1736-1740.
4. Kurochkina, N. & Lee, B. (1995). Hydrophobic potential by pairwise surface area sum. Protein Eng. 8, 437-442.
5. Hodes, Z.I., Némethy, G. & Scheraga, H.A. (1979). Model for the conformational analysis of hydrated peptides. Effect of hydration on the conformational stability of the terminally blocked residues of the 20 naturally occurring amino acids. Biopolymers 18, 1565-1610.
6. Augspurger, J.D. & Scheraga, H.A. (1996). An efficient, differentiable hydration potential for peptides and proteins. J. Comp. Chem. 17, 1549-1558.
7. Connolly, M.L. (1996). Molecular surfaces: a review. Network Sci. 2, http://www.netsci.org/Issues/1996/Apr/articles.html.
8. Dahiyat, B.I. & Mayo, S.L. (1996). Protein design automation. Protein Sci. 5, 895-903.
9. Creighton, T.E. (1993). Proteins: Structure and Molecular Properties. W.H. Freeman and Co., New York.
10. Richards, F.M. & Lim, W.A. (1994). An analysis of packing in the protein folding problem. Quart. Rev. Biophys. 26, 423-498.
11. Bernstein, P.C., et al., & Tasumi, M. (1977). The protein data bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.
12. Mayo, S.L., Olafson, B.D. & Goddard, W.A., III. (1990). Dreiding - a generic force-field for molecular simulations. J. Phys. Chem. 94, 8897-8909.
13. Dahiyat, B.I. & Mayo, S.L (1997). De novo protein design: fully automated sequence selection. Science 278, 82-87.
14. Connolly, M.L. (1983). Solvent accessible surfaces of proteins and nucleic acids. Science 221, 709-713.