Graphical visualization of mean hydration from molecular dynamics simulations

Journal of Molecular Graphics and Modelling

Volumn 15, Issue 6, 1997, Pages 355-358

  Pitera, Jed ^a   Kollman, Peter ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

(Hydroxymethyl)phenol; AMBER; Crown ether; Hydration visualization; MidasPlus; Molecular dynamics; N methyl acetamide; Sodium ion

Indexed keywords

BIOCHEMISTRY; COMPUTER SIMULATION; ETHERS; HYDRATION; IONS; MOLECULAR DYNAMICS; NUCLEIC ACIDS; PROTEINS; SOLVENTS; THREE DIMENSIONAL COMPUTER GRAPHICS; VISUALIZATION;

CROWN ETHER; HYDROXYMETHYL PHENOL; METHYL ACETAMIDE; SODIUM ION;

MOLECULAR STRUCTURE;

N METHYLACETAMIDE; NUCLEIC ACID; PROTEIN; SODIUM ION; WATER;

ARTICLE; CHEMICAL STRUCTURE; HYDRATION; MOLECULAR DYNAMICS; PRIORITY JOURNAL; SIMULATION;

ACETAMIDES; CATIONS, MONOVALENT; COMPUTER GRAPHICS; COMPUTER SIMULATION; CROWN ETHERS; ETHERS, CYCLIC; MODELS, MOLECULAR; PROBABILITY; SODIUM; WATER;

EID: 0031371171     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1093-3263(98)00006-0     Document Type: Article

References (15)

1. Lounnas, V., Pettitt, B., Findsen, L., and Subramanian, S. A microscopic view of protein solvation. J. Phys. Chem. 1992, 96, 7157-7159; Rudnicki, W., and Pettitt, B. Biopolymers 1997, 41, 107-119.
2. Lounnas, V., Pettitt, B., Findsen, L., and Subramanian, S. A microscopic view of protein solvation. J. Phys. Chem. 1992, 96, 7157-7159; Rudnicki, W., and Pettitt, B. Biopolymers 1997, 41, 107-119.
3. Subramanian P.S., Beveridge D.L. A theoretical study of the aqueous hydration of canonical B d(CGCGAATTCGCG) Monte Carlo simulation and comparison with crystallographic ordered water sites . J. Biomol. Struct. Dyn. 6:1989;1093-1122.
4. Meng E., Kollman P. Molecular dynamics studies of the properties of water around simple organic solutes. J. Phys. Chem. 100:1996;11460-11470.
5. Pearlman, D., Case, D., Caldwell, J., Ross, W., Cheatham, T., Ferguson, D., Seibel, G., Singh, U., Weiner, P., and Kollman, P. AMBER, version 4.1. University of California, San Francisco, San Francisco, California, 1995.
6. Cornell W., Cieplak P., Bayly C.I., Gould I.R., et al. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:1995;5179-5197.
7. Cornell W., Cieplak P., Bayly C.I., Kollman P. Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation. J. Am. Chem. Soc. 115:1993;9620-9631.
8. MidasPlus. Computer Graphics Laboratory, University of California, San Francisco, 1994. Supported by NIH RR-01081.
9. Huang C.C., Pettersen E.F., Klein T.E., Ferrin T.E., Langridge R. Conic A fast renderer for space-filling molecules with shadows . J. Mol. Graphics. 9:1991;230-236.
10. Ranghino G., Romano S., Lehn J.M., Wipff G. Monte Carlo study of the conformation-dependent hydration of the 18-crown-6 macrocycle. J. Am. Chem. Soc. 107:1985;7873-7877.
11. Ben-Naim, A. Solvent-induced interactions: Hydrophobic and hydrophilic phenomena. J. Chem. Phys. 1989, 90, 7412-7425; Ben-Naim, A. Solvent effects on protein association and protein folding. Biopolymers 1990, 29, 567-596.
12. Ben-Naim, A. Solvent-induced interactions: Hydrophobic and hydrophilic phenomena. J. Chem. Phys. 1989, 90, 7412-7425; Ben-Naim, A. Solvent effects on protein association and protein folding. Biopolymers 1990, 29, 567-596.
13. Sun Y., Kollman P. Are there water-bridge-induced hydrophilic interactions. J. Phys. Chem. 100:1996;6760-6763.
14. Cheatham T., Crowley M., Fox T., Kollman P. A molecular level picture of the stabilization of A-DNA in mixed ethanol-water solutions. Proc. Natl. Acad. Sci. U.S.A. 94:1997;9626-9630.
15. Miller, J. Unpublished results.