Efficient calculation of relative binding free energies by umbrella sampling perturbation

Journal of Computational Chemistry

Volumn 35, Issue 31, 2014, Pages 2256-2262

  Zeller, Fabian ^a   Zacharias, Martin ^a  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

alanine scan; drug design; free energy perturbation; ligand receptor binding; molecular dynamics simulation; potential of mean force

Indexed keywords

AMINO ACIDS; ASSOCIATION REACTIONS; CHEMICAL MODIFICATION; FREE ENERGY; MOLECULAR DYNAMICS; MOLECULES; PLASMA INTERACTIONS; REACTION KINETICS; SOLUTIONS;

ALANINE SCAN; DRUG DESIGN; FREE ENERGY PERTURBATION; LIGAND-RECEPTOR BINDING; MOLECULAR DYNAMICS SIMULATIONS; POTENTIAL OF MEAN FORCE;

BINDING ENERGY;

ALANINE; PEPTIDE; PROTEIN BINDING;

CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; THERMODYNAMICS;

ALANINE; COMPUTER SIMULATION; MODELS, MOLECULAR; PEPTIDES; PROTEIN BINDING; THERMODYNAMICS;

EID: 84931477990     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.23744     Document Type: Article

References (33)

1. G. M. Torrie, J. P. Valleau, J. Comput. Phys. 1977, 23, 187.
2. W. L. Jorgensen, J. Am. Chem. Soc. 1989, 111, 3770.
3. H.-J. Woo, B. Roux, Proc. Natl. Acad. Sci. USA 2005, 102, 6825.
4. J. C. Gumbart, B. Roux, C. Chipot, J. Chem. Theory Comput. 2013, 9, 3789.
5. F. Zeller, M. Zacharias, J. Chem. Theory Comput. 2014, 10, 703.
6. M. Gilson, J. Given, B. Bush, J. McCammon, Biophys. J. 1997, 72, 1047.
7. G. König, S. Bruckner, S. Boresch, J. Comput. Chem. 2009, 30, 1712.
8. H. Liu, A. E. Mark, W. F. van Gunsteren, J. Phys. Chem. 1996, 100, 9485.
9. Z. Lin, J. Kornfeld, M. Mächler, W. F. van Gunsteren, J. Am. Chem. Soc. 2010, 132, 7276.
10. J. Srinivasan, T. E. Cheatham, P. Cieplak, P. A. Kollman, D. A. Case, J. Am. Chem. Soc. 1998, 120, 9401.
11. J. Åqvist, C. Medina, J.-E. Samuelsson, Protein Eng. Des. Sel. 1994, 7, 385.
12. R. W. Zwanzig, J. Chem. Phys. 1954, 22, 1420.
13. M. Pazgier, M. Liu, G. Zou, W. Yuan, C. Li, C. Li, J. Li, J. Monbo, D. Zella, S. G. Tarasov, W. Lu, Proc. Natl. Acad. Sci. USA 2009, 106, 4665.
14. A. M. Ferrenberg, R. H. Swendsen, Phys. Rev. Lett. 1989, 63, 1195.
15. S. Kumar, J. M. Rosenberg, D. Bouzida, R. H. Swendsen, P. A. Kollman, J. Comput. Chem. 1992, 13, 1011.
16. W. L. Jorgensen, J. Am. Chem. Soc. 1989, 111, 3770.
17. B. Roux, Comput. Phys. Commun. 1995, 91, 275.
18. H. Nguyen, D. R. Roe, C. Simmerling, J. Chem. Theory Comput. 2013, 9, 2020.
19. D. A. Case, T. A. Darden, T. E. Cheatham III, C. L. Simmerling, J. Wang, R. E. Duke, R. Luo, R. C. Walker, W. Zhang, K. M. Merz, B. Roberts, S. Hayik, A. Roitberg, G. Seabra, J. Swails, A. W. Götz, I. Kolossváry, K. F. Wong, F. Paesani, J. Vanicek, R. M. Wolf, J. Liu, X. Wu, S. R. Brozell, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, J. Wang, M.-J. Hsieh, G. Cui, D. R. Roe, D. H. Mathews, M. G. Seetin, R. Salomon-Ferrer, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, and, P. A. Kollman, AMBER12; University of California, San Francisco, CA, 2012.
20. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, M. L. Klein, J. Chem. Phys. 1983, 79, 926.
21. W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, P. A. Kollman, J. Am. Chem. Soc. 1995, 117, 5179.
22. D. Sitkoff, K. A. Sharp, B. Honig, J. Phys. Chem. 1994, 98, 1978.
23. J. Weiser, P. S. Shenkin, W. C. Still, J. Comput. Chem. 1999, 20, 217.
24. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola, J. R. Haak, J. Chem. Phys. 1984, 81, 3684.
25. R. W. Pastor, B. R. Brooks, A. Szabo, Mol. Phys. 1988, 65, 1409.
26. J.-P. Ryckaert, G. Ciccotti, H. J. Berendsen, J. Comput. Phys. 1977, 23, 327.
27. Y. Sugita, A. Kitao, Y. Okamoto, J. Chem. Phys. 2000, 113, 6042.
28. J. C. Gumbart, B. Roux, C. Chipot, J. Chem. Theory Comput. 2013, 9, 794.
29. A. Grossfield, WHAM: The Weighted Histogram Analysis Method 2.0.7; Grossfield Lab: Rochester, NY, 2013.
30. I. Massova, P. A. Kollman, J. Am. Chem. Soc. 1999, 121, 8133.
31. C. Li, M. Pazgier, C. Li, W. Yuan, M. Liu, G. Wei, W.-Y. Lu, W. Lu, J. Mol. Biol. 2010, 398, 200.
32. Y. Liu, D. Lane, C. Verma, Theor. Chem. Acc. 2011, 130, 1145.
33. F. Zeller, M. Zacharias, J. Phys. Chem. B 2014, 118, 7467.