Calculation of absolute protein-ligand binding free energy using distributed replica sampling

Journal of Chemical Physics

Volumn 129, Issue 15, 2008, Pages

  Rodinger, Tomas ^a,b,c,d   Howell, P Lynne ^a,b   Pom̀s, Ŕgis ^a,b  

^a HOSPITAL FOR SICK CHILDREN   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

^c UNIVERSITY OF TORONTO   (Canada)

^d Zymeworks Inc   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATION THEORY; DISTRIBUTED COMPUTER SYSTEMS; FREE ENERGY; LIGANDS; MOLECULAR PHYSICS; PLASMA INTERACTIONS; POTENTIAL ENERGY; PROTEINS; QUANTUM CHEMISTRY;

EFFICIENT IMPLEMENTATION; GENERALIZED HAMILTONIANS; HETEROGENEOUS COMPUTING; LARGE SCALE SIMULATIONS; POTENTIAL OF MEAN FORCE; REPLICA EXCHANGE METHOD; STATISTICAL CONVERGENCE; THERMODYNAMIC INTEGRATION;

BINDING ENERGY;

BENZENE; LIGAND; LYSOZYME;

ALGORITHM; ARTICLE; BACTERIOPHAGE T4; CHEMICAL MODEL; CHEMISTRY; COMPUTER; CONFORMATION; ENZYMOLOGY; METABOLISM; PROTEIN BINDING; QUALITY CONTROL; STATISTICS; THERMODYNAMICS;

ALGORITHMS; BACTERIOPHAGE T4; BENCHMARKING; BENZENE; COMPUTERS; LIGANDS; MODELS, CHEMICAL; MOLECULAR CONFORMATION; MURAMIDASE; PROTEIN BINDING; STOCHASTIC PROCESSES; THERMODYNAMICS;

EID: 54849417403     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2989800     Document Type: Article

References (59)

1. T. Rodinger and R. Pom̀s, Curr. Opin. Struct. Biol. 15, 164 (2005).
2. I. Andricioaei, D. Asthagiri, T. L. Beck, C. Chipot, E. Darve, C. Dellago, G. Hummer, N. Lu, A. E. Mark, A. Z. Panagiotopoulos, V. S. Pande, A. Pohorille, L. R. Pratt, M. S. Shell, T. Simonson, and T. B. Woolf, in Free Energy Calculations: Theory and Applications in Chemistry and Biology, edited by, C. Chipot, and, A. Pohorille, (Springer-Verlag, Berlin, 2007).
3. C. Chipot and D. A. Pearlman, Mol. Simul. 28, 1 (2002).
4. W. F. van Gunsteren, X. Daura, and A. E. Mark, Helv. Chim. Acta 85, 3113 (2002).
5. T. Simonson, G. Archontis, and M. Karplus, Acc. Chem. Res. 35, 430 (2002).
6. L. Kale, R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, N. Krawetz, J. Phillips, A. Shinozaki, K. Varadarajan, and K. Schulten, J. Comput. Phys. 151, 283 (1999).
7. K. Y. Sanbonmatsu, S. Joseph, and C. S. Tung, Proc. Natl. Acad. Sci. U.S.A. 102, 15854 (2005).
8. P. L. Freddolino, A. S. Arkhipov, S. B. Larson, A. McPherson, and K. Schulten, Structure (London) 14, 437 (2006).
9. E. J. Sorin, Y. M. Rhee, M. R. Shirts, and V. S. Pande, J. Mol. Biol. 356, 248 (2006).
10. B. A. Berg and T. Neuhaus, Phys. Lett. B 267, 249 (1991).
11. A. P. Lyubartsev, A. A. Martsinovski, S. V. Shevkunov, and P. N. Vorontsovvelyaminov, J. Chem. Phys. 96, 1776 (1992).
12. E. Marinari and G. Parisi, Europhys. Lett. 19, 451 (1992).
13. K. Hukushima and K. Nemoto, J. Phys. Soc. Jpn. 65, 1604 (1996).
14. Y. Sugita and Y. Okamoto, Chem. Phys. Lett. 314, 141 (1999).
15. M. C. Tesi, E. J. J. van Rensburg, E. Orlandini, and S. G. Whittington, J. Stat. Phys. 82, 155 (1996).
16. A. Mitsutake and Y. Okamoto, J. Chem. Phys. 121, 2491 (2004).
17. A. Mitsutake and Y. Okamoto, Chem. Phys. Lett. 332, 131 (2000).
18. A. Mitsutake, Y. Sugita, and Y. Okamoto, J. Chem. Phys. 118, 6676 (2003).
19. A. Mitsutake, Y. Sugita, and Y. Okamoto, J. Chem. Phys. 118, 6664 (2003).
20. Y. Sugita, A. Kitao, and Y. Okamoto, J. Chem. Phys. 113, 6042 (2000).
21. Y. Sugita and Y. Okamoto, Chem. Phys. Lett. 329, 261 (2000).
22. A. E. García and J. N. Onuchic, Proc. Natl. Acad. Sci. U.S.A. 100, 13898 (2003).
23. H. Nymeyer and A. E. García, Proc. Natl. Acad. Sci. U.S.A. 100, 13934 (2003).
24. D. Paschek and A. E. García, Phys. Rev. Lett. 93, 238105 (2004).
25. A. E. García and K. Y. Sanbonmatsu, Proteins 42, 345 (2001).
26. S. Gnanakaran, H. Nymeyer, J. Portman, K.-Y. Sanbonmatsu, and A. E. García, Curr. Opin. Struct. Biol. 13, 168 (2003).
27. R. W. Zwanzig, J. Chem. Phys. 22, 1420 (1954).
28. J. G. Kirkwood, J. Chem. Phys. 3, 300 (1935).
29. G. M. Torrie and J. P. Valleau, Chem. Phys. Lett. 28, 578 (1974).
30. M. R. Shirts, J. W. Pitera, W. C. Swope, and V. S. Pande, J. Chem. Phys. 119, 5740 (2003).
31. T. Rodinger, P. L. Howell, and R. Pom̀s, J. Chem. Phys. 123, 034104 (2005).
32. T. Rodinger, P. L. Howell, and R. Pom̀s, J. Chem. Theory Comput. 2, 725 (2006).
33. C. Neale, T. Rodinger, and R. Pom̀s, Chem. Phys. Lett. 460, 375 (2008).
34. D. L. Mobley, J. D. Chodera, and K. A. Dill, J. Chem. Phys. 125, 084902 (2006).
35. G. Jayachandran, M. R. Shirts, S. Park, and V. S. Pande, J. Chem. Phys. 125, 084901 (2006).
36. E. Darve and A. Pohorille, J. Chem. Phys. 115, 9169 (2001).
37. E. Darve, M. A. Wilson, and A. Pohorille, Mol. Simul. 28, 113 (2002).
38. J. H́nin and C. Chipot, J. Chem. Phys. 121, 2904 (2004).
39. M. Mezei, J. Comput. Phys. 68, 237 (1987).
40. C. Bartels and M. Karplus, J. Comput. Chem. 18, 1450 (1997).
41. C. J. Woods, J. W. Essex, and M. A. King, J. Phys. Chem. B 107, 13703 (2003).
42. A. Morton, W. A. Baase, and B. W. Matthews, Biochemistry 34, 8564 (1995).
43. A. Morton and B. W. Matthews, Biochemistry 34, 8576 (1995).
44. R. Pom̀s, E. Eisenmesser, C. B. Post, and B. Roux, J. Chem. Phys. 111, 3387 (1999).
45. B. O. Brandsdal and A. O. Smalas, Protein Eng. 13, 239 (2000).
46. D. Trzesniak, A. P. E. Kunz, and W. F. van Gunsteren, ChemPhysChem 8, 162 (2007).
47. M. K. Gilson, J. A. Given, B. L. Bush, and J. A. McCammon, Biophys. J. 72, 1047 (1997).
48. J. A. McCammon, Curr. Opin. Struct. Biol. 8, 245 (1998).
49. S. Boresch, F. Tettinger, M. Leitgeb, and M. Karplus, J. Phys. Chem. B 107, 9535 (2003).
50. M. D. Collins, G. Hummer, M. L. Quillin, B. W. Matthews, and S. M. Gruner, Proc. Natl. Acad. Sci. U.S.A. 102, 16668 (2005).
51. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem. 4, 187 (1983).
52. A. D. MacKerell, Jr., D. Bashford, M. Bellott, R. L. Dunbrack, Jr., J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiórkiewicz-Kuczera, D. Yin, and M. Karplus, J. Phys. Chem. B 102, 3586 (1998).
53. W. Yang, R. Bitetti-Putzer, and M. Karplus, J. Chem. Phys. 120, 2618 (2004).
54. Y. Q. Deng and B. Roux, J. Phys. Chem. B 108, 16567 (2004).
55. J. L. Maccallum and D. P. Tieleman, J. Comput. Chem. 24, 1930 (2003).
56. Y. Q. Deng and B. Roux, J. Chem. Theory Comput. 2, 1255 (2006).
57. J. Hermans and L. Wang, J. Am. Chem. Soc. 119, 2707 (1997).
58. J. Hine and P. K. Mookerjee, J. Org. Chem. 40, 292 (1975).
59. G. D. Smith, PROFIT, a locally written program for orienting one protein molecule onto another by a least-squares procedure, Hauptman-Woodward Medical Research Institute, Buffalo, NY, 1993.