Implicit solvation parameters derived from explicit water forces in large-scale molecular dynamics simulations

Journal of Chemical Theory and Computation

Volumn 8, Issue 7, 2012, Pages 2391-2403

  Kleinjung, Jens ^a   Scott, Walter R P ^b   Allison, Jane R ^c   Van Gunsteren, Wilfred F ^c   Fraternali, Franca ^d  

^a NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^c ETH ZURICH   (Switzerland)

^d KING'S COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84863669964     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct200390j     Document Type: Article

References (50)

1. Schiffer, C. A.; Dötsch, V. Curr. Opin. Biotechnol. 1996, 7, 428-432
2. De Simone, A.; Dodson, G. G.; Verma, C. S.; Zagari, A.; Fraternali, F. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 7535-7540
3. De Simone, A.; Spadaccini, R.; Temussi, P. A.; Fraternali, F. Biophys. J. 2006, 90, 3052-3061
4. Autore, F.; Bergeron, J. R. C.; Malim, M. H.; Fraternali, F.; Huthoff, H. PLoS One 2010, 5, e11515
5. Kleinjung, J.; Bayley, P. M.; Fraternali, F. FEBS Lett. 2000, 470, 257-262
6. Kleinjung, J.; Fraternali, F.; Martin, S. R.; Bayley, P. M. Proteins 2003, 50, 648-656
7. Gaudreault, M.; Viñals, J. Phys. Rev. E 2009, 80, 021916
8. Arnautova, Y. A.; Vorobjev, Y. N.; Vila, J. A.; Scheraga, H. A. Proteins 2009, 77, 38-51
9. Lazaridis, T.; Karplus, M. Curr. Opin. Struct. Biol. 2000, 10, 139-145
10. am Busch, M. S.; Lopes, A.; Amara, N.; Bathelt, C.; Simonson, T. BMC Bioinf. 2008, 9, 148
11. Lazaridis, T. Proteins 2005, 58, 518-527
12. Ulmschneider, M. B.; Ulmschneider, J. P.; Sansom, M. S. P.; Di Nola, A. Biophys. J. 2007, 92, 2338-2349
13. Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. J. Am. Chem. Soc. 1990, 112, 6127-6129
14. Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G. J. Phys. Chem. 1996, 100, 19824-19839
15. Onufriev, A.; Bashford, D.; Case, D. A. J. Phys. Chem. B 2000, 104, 3712-3720
16. Gallicchio, E.; Levy, R. M. J. Comput. Chem. 2004, 25, 479-499
17. Feig, M.; Onufriev, A.; Lee, M. S.; Im, W.; Case, D. A.; Brooks, C. L. J. Comput. Chem. 2004, 25, 265-284
18. Shimizu, S.; Chan, H. S. Proteins 2002, 48, 15-30
19. Lee, B.; Richards, F. M. J. Mol. Biol. 1971, 55, 379-400
20. Prabhu, N. V.; Zhu, P.; Sharp, K. A. J. Comput. Chem. 2004, 25, 2049-2064
21. Wagoner, J.; Baker, N. A. J. Comput. Chem. 2004, 25, 1623-1629
22. Vitalis, A.; Pappu, R. V. J. Comput. Chem. 2009, 30, 673-699
23. Chen, J.; Brooks, C. L. Phys. Chem. Chem. Phys. 2008, 10, 471-481
24. Allison, J. R.; Boguslawski, K.; Fraternali, F.; van Gunsteren, W. F. J. Phys. Chem. B 2011, 115, 4547-4557
25. Levy, R. M.; Zhang, L. Y.; Gallicchio, E.; Felts, A. K. J. Am. Chem. Soc. 2003, 125, 9523-9530
26. Wagoner, J.; Baker, N. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 8331-8336
27. Fraternali, F.; van Gunsteren, W. F. J. Mol. Biol. 1996, 256, 939-948
28. Hasel, W.; Hendrickson, T.; Still, W. C. Tetrahedron Comput. Methodol. 1988, 1, 103-116
29. van Gunsteren, W. F.; Billeter, S. R.; Eising, A. A.; Hünenberger, P. H.; Krüger, P.; Mark, A. E.; Scott, W. R. P.; Tironi, I. G. Biomolecular Simulation: The GROMOS96 Manual and User Guide; vdf Hochschulverlag AG an der ETH Zürich and BIOMOS b.v.: 1996
30. Christen, M.; Hünenberger, P. H.; Bakowies, D.; Baron, R.; Bürgi, R.; Geerke, D. P.; Heinz, T. N.; Kastenholz, M. A.; Kräutler, V.; Oostenbrink, C.; Peter, C.; Trzesniak, D.; van Gunsteren, W. F. J. Comput. Chem. 2005, 26, 1719-1751
31. Ferrara, P.; Apostolakis, J.; Caflisch, A. Proteins 2002, 46, 24-33
32. Yun-yu, S.; Lu, W.; van Gunsteren, W. F. Mol. Simul. 1988, 1, 369-383
33. van Gunsteren, W. F.; Berendsen, H. J. C. Mol. Simul. 1988, 1, 173-185
34. Daura, X.; Mark, A. E.; van Gunsteren, W. F. J. Comput. Chem. 1998, 19, 535-547
35. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. Intermolecular Forces, 1 st ed.; Pullman, B., Ed.; Reidel; Dordrecht, 1981; Chapter Interaction models for water in relation to protein hydration, pp 331-342
36. Martin, A. C. Protein Eng. 2000, 13, 829-837
37. Kamat, A. P.; Lesk, A. M. Proteins 2007, 66, 869-876
38. Brenner, S. E.; Koehl, P.; Levitt, M. Nucleic Acids Res. 2000, 28, 254-256
39. Pandini, A.; Bonati, L.; Fraternali, F.; Kleinjung, J. Bioinformatics 2007, 23, 515-516
40. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Di Nola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684-3690
41. Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. C. J. Chem. Phys. 1977, 23, 327-341
42. Fraternali, F.; Cavallo, L. Nucleic Acids Res. 2002, 30, 2950-2960
43. R Development Core Team, R: A Language and Environment for Statistical Computing; R Foundation for Statistical Computing: Vienna, Austria, 2009
44. Venables, W. N.; Ripley, B. D. Modern Applied Statistics with S, 4 th ed.; Springer: 2002
45. Skiena, S. S. The Algorithm Design Manual, 2 nd ed.; Springer: 2008; Chapter 8.5, pp 294-298
46. Cover, T. M.; Thomas, J. A. Elements of Information Theory; Wiley Series in Telecommunication; Wiley: 1991
47. Canty, A. S. An S-Plus Library for Resampling Methods. 30th Symposium on the Interface: Computing Science and Statistics, 1998
48. Martin, L. C.; Gloor, G. B.; Dunn, S. D.; Wahl, L. M. Bioinformatics 2005, 21, 4116-4124
49. Pandini, A.; Fornili, A.; Kleinjung, J. BMC Bioinf. 2010, 11, 97
50. Pandini, A.; Fornili, A.; Fraternali, F.; Kleinjung, J. FASEB J. 2012, 26, 868-881