New Born radii deriving method for generalized born model

Journal of Chemical Information and Modeling

Volumn 45, Issue 1, 2005, Pages 88-93

  Zhang, Wei ^a   Hou, Tingjun ^a   Xu, Xiaojie ^a  

^a PEKING UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; BIOPOLYMERS; CONTINUUM MECHANICS; DATABASE SYSTEMS; MOLECULAR DYNAMICS; PHASE SHIFT; PROTEINS; SURFACE PHENOMENA;

BORN MODEL; BORN RADII; ORGANIC MOLECULES; SOLVATION;

FREE ENERGY;

EID: 19644373355     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci0497408     Document Type: Article

References (25)

1. Rossky, P. J.; Karplus, M. Solvation. A Molecular Dynamics Study of a Dipeptide in Water. J. Am. Chem. Soc. 1979, 101, 1913-1937.
2. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 1983, 79, 926-935.
3. Jorgensen, W. L.; Ravimohan, C. J. Monte Carlo simulation of differences in free energies of hydration. J. Chem. Phys. 1985, 83, 3050-3054.
4. Eisenberg, D.; McLachlan, A. D. Solvation Energy in Protein Folding and Binding. Nature 1986, 319, 199-203.
5. Ooi. T.; Oobatake, M.; Nemethy, G.; Scheraga, H. A. Accessible Surface Areas as a Measure of the Thermodynamic Parameters of Hydration of Peptides. Proc. Natl. Acad. Sci. U.S.A. 1987, 84, 3086-3090.
6. Kang, Y. K.; Nemethy, G.; Scheraga, H. A. Free energy of hydration of solute molecules. 1. Improvement of the hydration shell model by exact computations of overlapping volumes. J. Phys. Chem. 1987, 91, 4105-4109.
7. Application of the hydration shell model to nonionic organic molecules. 4109-4118.
8. Kang, Y. K.; Nemethy, G.; Scheraga, H. A. Free energies of hydration of solute molecules. 3. Application of the hydration shell model to charged organic molecules J. Phys. Chem. 1987, 91, 4118-4122.
9. Gilson, M.; Honig, B. Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis. Proteins 1988, 4, 7-18.
10. Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. J. A General Treatment of Solvation for Molecular Mechanics. J. Am. Chem. Soc. 1990, 112, 6127-6133.
11. Cramer, C. J.; Truhlar, D. G. General Parametrized SCF Model for Free Energies of Solvation in Aqueous Solution. J. Am. Chem. Soc. 1991, 113, 8305-8311.
12. Qiu, D.; Shenkin, P. S.; Hollinger, F. P.; Still, W. C. The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii. J. Phys. Chem. A 1997, 101, 3005-3014.
13. Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G. Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium. J. Phys. Chem. 1996, 100, 19824-39.
14. Schaefer, M.; Karplus, M. A comprehensive analytical treatment of continuum electrostatics. J. Phys. Chem. 1996, 100, 1578-1599.
15. Jayaram, B.; Sprous, D.; Beveridge, D. L. Solvation Free Energy of Biomacromolecules: Parameters for a Modified Generalized Born Model Consistent with the AMBER Force Field. J. Phys. Chem. 1998, 102, 9571-9576
16. Zhang W.; Hou, T. J.; Qiao X. B.; Xu X. J. Parameters for the Generalized Born Model Consistent with RESP Atomic Partial Charge Assignment Protocol. J. Phys. Chem. B 2003, 107, 9071-9078.
17. Cheng, A.; Best, S. A.; Merz, J. K. M.; Reynolds, C. H. GB/SA water model for the Merck molecular force field (MMFF). J. Mol. Graph. Mod. 2000, 18, 273-282.
18. Zhu, J.; Shi Y. Y.; Liu, H. Y. Parametrization of a Generalized Born/Solvent-Accessible Surface Area Model and Applications to the Simulation of Protein Dynamics. J. Phys. Chem. B 2002, 106, 4844-4853.
19. Ullmann, J. R. An algorithm for subgraph isomorphism. J. As. Com. Ma 1976, 23, 31-42.
20. Lee, B.; Richards, F. M. The interpretation of protein structures: Interpretation of static accessibility. J. Mol. Biol. 1971, 55, 379-400.
21. Zhang, W.; Hou, T.; Qiao, X.; Xu, X. Some Basic Data Structures and Algorithms for Chemical Generic Programming. J. Chem. Inf. Comput. Sci. 2004, in press.
22. Gaussian 98 (Revision A.3), M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, V. G. Zakrzewski, J. A. Montgomery, Jr., R. E. Stratmann, J. C. Burant, S. Dapprich, J. M. Millam, A. D. Daniels, K. N. Kudin, M. C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G. A. Petersson, P. Y. Ayala, Q. Cui, K. Morokuma, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. Cioslowski, J. V. Ortiz, A. G. Baboul, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, C. Gonzalez, M. Challacombe, P. M. W. Gill, B. G. Johnson, W. Chen, M. W. Wong, J. L. Andres, M. Head-Gordon, E. S. Replogle, J. A. Pople, Gaussian, Inc., Pittsburgh, PA, 1998.
23. Honig, B.; Sharp, K.; Yang, A.-S. Macroscopic models of aqueous solutions: Biological and chemical appications. J. Phys. Chem. 1993, 97, 1101-1109.
24. Sitkoff, D.; Sharp, K. A.; Honig, B. Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models. J. Phys. Chem. 1994, 98, 1978-1988.
25. Onufriev, A.; Case, D. A.; Bashford, D. Effective Born radii in the generalized Born approximation: The importance of being perfect. J. Comput. Chem. 2002, 25(14), 1297-1304.