A new analytical method for computing solvent-accessible surface area of macromolecules and its gradients

Journal of Computational Chemistry

Volumn 26, Issue 4, 2005, Pages 334-343

  Hayryan, Shura ^a   Hu, Chin Kun ^a   Skřivánek, Jaroslav ^b   Hayryan, Edik ^c   Pokorný, Imrich ^b  

^a INSTITUTE OF PHYSICS   (Taiwan)

^b TECHNICAL UNIVERSITY OF KO ICE   (Slovakia)

^c JOINT INSTITUTE FOR NUCLEAR RESEARCH   (Russian Federation)

Author keywords

Analytical gradients; Projection onto the plane; Proteins; SMMP; Solvation energy; Solvent accessible surface area

Indexed keywords

ALGORITHMS; CONFORMATIONS; PROTEINS; SOLUTIONS; SOLVENTS; THERMODYNAMIC PROPERTIES;

ANALYTICAL GRADIENTS; PROJECTION ONTO THE PLANE; SMMP; SOLVATION ENERGY; SOLVENT-ACCESSIBLE SURFACE AREA;

MACROMOLECULES;

PROTEIN;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; MACROMOLECULE; SURFACE PROPERTY; THERMODYNAMICS;

ALGORITHMS; COMPUTER SIMULATION; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; PROTEINS; SURFACE PROPERTIES; THERMODYNAMICS;

EID: 14744271380     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcc.20125     Document Type: Article

References (46)

1. Eisenberg, D.; McLachlan, A. D. Nature 1986, 316, 199.
2. Lee, B.; Richards, F. M. J Mol Biol 1971, 55, 379.
3. Richards, F. M. Annu Rev Biophys Bioeng 1977, 6, 151.
4. Connolly, M. L. J Appl Crystallogr 1983, 16, 548.
5. Richmond, T. J. J Mol Biol 1984, 178, 63.
6. Connolly, M. L. J Appl Crystallogr 1985, 18, 499.
7. Gibson, K. D.; Scheraga, H. A. Mol Phys 1988, 64, 641.
8. Perrot, C.; Cheng, B.; Gibson, K. D.; Vila, J.; Palmer, K. A.; Nayeem, A.; Maigret, B.; Scheraga, H. A. J Comp Chem 1992, 13, 1.
9. Eisenhaber, F.; Argos, P. J Comp Chem 1993, 14, 1272.
10. Fraczkiewicz, R.; Braun, W. J Comp Chem 1998, 19, 319.
11. Shrake, A.; Rupley, J. A. J Mol Biol 1973, 79, 351.
12. Richmond, T. J.; Richards, F. M. J Mol Biol 1978, 129, 527.
13. Sila, E.; Tunom, I.; Pascual-Ahuir, J. L. J Comp Chem 1991, 12, 1077.
14. Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendricson, T. J Am Chem Soc 1990, 112, 6127.
15. Eisenhaber, F.; Lijnzaad, Ph.; Argos, P.; Sander, C.; Scharf, M. J Comp Chem 1995, 16, 273.
16. Masuya, M.; Doi, J. J Mol Graphics 1995, 13, 331.
17. Braun, W. In Computer Simulation of Biomolecular Systems; van Gunsteren, W.; Weener, P.; Wilkinson, T., Eds.; ESCOM: Laiden, 1996, vol. 3.
18. Berg, B. A.; Neuhaus, T. J Phys Chem 1995, 99, 11276.
19. Hukushima, K.; Nemoto, K. J Phys Soc Jpn 1996, 65, 1604.
20. Geyer, G. J.; Tompson, E. A. J Am Stat Assoc 1995, 90, 909.
21. Hansmann, U. H. E.; Okamoto, Y. J Comp Chem 1993, 14, 1333.
22. Hamnsmann, U. H. E.; Masuya, M.; Okamoto, Y. Proc Natl Acad Sci USA 1997, 94, 10652.
23. Hansmann, U. H. E.; Wille, L. Phys Rev Lett 2002, 88, 068105.
24. Eisenmenger, F.; Hansmann, U. H. E.; Hayryan, Sh.; Hu, C. K. Comp Phys Commun 2001, 138, 193.
25. Hayryan, S.; Hu, C.-K.; Hu, S.-Y.; Shang, R.-J. J Comp Chem 2001, 22, 1287.
26. Lin, C.-Y.; Hu, C.-K.; Hansmann, U. H. E. Proteins Struct Funct Genet 2003, 52, 436.
27. Peng, Y.; Hansmann, U. H. E. Biophys J 2002, 82, 3269.
28. Peng, Y.; Hansmann, U. H. E. J Chem Phys 2003, 118, 2374.
29. Berg, B. A.; Hsu, H.-P. Phys Rev E 2004, 69, 026703.
30. Do Carmo, M. P. In Differential Geometry of Curves and Surfaces; Prentice-Hall: Englewood Cliffs, NJ, Jersey, 1976.
31. Klepeis, J. L.; Floudas, C. A. J Comp Chem 1999, 20, 636.
32. Ooi, T., et al. Proc Natl Acad Sci USA 1987, 8, 3086.
33. Vila, J., et al. Proteins Struct Funct Genet 1991, 10, 199.
34. Wesson, L.; Eisenberg, D. Protein Sci 1992, l, 227.
35. Eisenberg, D.; Mclachlan, A. D. Nature 1986, 319, 199.
36. Schiffer, C. A., et al. Mol Simul 1993, 10, 121.
37. von Freyberg, B.; Braun, W. J Comp Chem 1993, 14, 510.
38. Busa, J., et al. Comp Phys Commun, 2005, 165, 59.
39. Hu, C.-K.; Lin, C.-Y.; Chen, J.-A. Phys Rev Lett 1995, 75, 193 and 2786 (E).
40. Hu, C.-K.; Lin, C.-Y.; Chen, J.-A. Phys A 1995, 221, 80.
41. Hu, C.-K.; Lin, C.-Y. Phys Rev Lett 1996, 77, 8.
42. Hu, C.-K.; Wang, F.-G. J Korean Phys Soc 1997, 31, S271.
43. Lin, C.-Y.; Hu, C.-K. Phys Rev E 1998, 58, 1521.
44. Hsu, H. P.; Lin, S. C.; Hu, C.-K. Phys Rev E 2001, 64, 016127.
45. Watanabe, H., et al. J Phys Soc Jpn 2001, 70, 1537.
46. Watanabe, H.; Yukawa, S.; Ito, N.; Hu, C.-K. Phys Rev Lett 2004, 93, 190601.