Adaptive biasing combined with hamiltonian replica exchange to improve umbrella sampling free energy simulations

Journal of Chemical Theory and Computation

Volumn 10, Issue 2, 2014, Pages 703-710

  Zeller, Fabian ^a   Zacharias, Martin ^a  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84894152562     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct400689h     Document Type: Article

References (30)

1. Free energy calculations: Theory and Applications in Chemistry and Biology; Chipot, C., Pohorille, A., Eds.; Springer: New York, 2007.
2. Woo, H.-J.; Roux, B. Calculation of absolute protein-ligand binding free energy from computer simulations Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6825-6830
3. Boresch, S.; Tettinger, F.; Leitgeb, M.; Karplus, M. Absolute Binding Free Energies: A Quantitative Approach for their Calculation J. Phys. Chem. B 2003, 107, 9535-9551
4. Rodinger, T.; Howell, P. L.; Pomes, R. Absolute free energy calculations by thermodynamic integration in four spatial dimensions J. Chem. Phys. 2005, 123, 034-104
5. Ytreberg, F. M.; Zuckerman, D. M. Simple estimation of absolute free energies for biomolecules J. Chem. Phys. 2006, 124, 104-105
6. Deng, Y.; Roux, B. Computations of Standard Binding Free Energies with Molecular Dynamics Simulations J. Phys. Chem. B 2009, 113, 2234-2246
7. Buelens, F. P.; Grubmüller, H. Linear-scaling soft-core scheme for alchemical free energy calculations J. Comput. Chem. 2012, 33, 25-33
8. Luitz, M. P.; Zacharias, M. Role of tyrosine hot-spot residues at the interface of colicin E9 and immunity protein 9: A comparative free energy simulation study Proteins: Struct., Funct., Bioinf. 2013, 81, 461-468
9. Gilson, M. K.; Given, J. A.; Bush, B. L.; McCammon, J. A. The statistical-thermodynamic basis for computation of binding affinities: a critical review Biophys. J. 1997, 72, 1047-1069
10. Fujitani, H.; Tanida, Y.; Ito, M.; Jayachandran, G.; Snow, C. D.; Shirts, M. R.; Sorin, E. J.; Pande, V. S. Direct calculation of the binding free energies of FKBP ligands J. Chem. Phys. 2005, 123, 084108
11. Lee, M. S.; Olson, M. A. Calculation of Absolute Protein-Ligand Binding Affinity Using Path and Endpoint Approaches Biophys. J. 2006, 90, 864-877
12. Shirts, M. R.; Pitera, J. W.; Swope, W. C.; Pande, V. S. Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins J. Chem. Phys. 2003, 119, 5740-5761
13. Mobley, D. L.; Bayly, C. I.; Cooper, M. D.; Shirts, M. R.; Dill, K. A. Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations J. Chem. Theory Comput. 2009, 5, 350-358
14. Jiang, W.; Roux, B. Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations J. Chem. Theory Comput. 2010, 6, 2559-2565
15. Gumbart, J. C.; Roux, B.; Chipot, C. Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy? J. Chem. Theory Comput. 2013, 9, 794-802
16. Torrie, G. M.; Valleau, J. P. Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling J. Comput. Phys. 1977, 23, 187-199
17. Jorgensen, W. L. Interactions between amides in solution and the thermodynamics of weak binding J. Am. Chem. Soc. 1989, 111, 3770-3771
18. Laio, A.; Parrinello, M. Escaping free-energy minima Proc. Natl. Acad. Sci. U. S. A. 2002, 99, 12562-12566
19. Darve, E.; Pohorille, A. Calculating free energies using average force J. Chem. Phys. 2001, 115, 9169-9183
20. Babin, V.; Roland, C.; Sagui, C. Adaptively biased molecular dynamics for free energy calculations J. Chem. Phys. 2008, 128, 134101
21. Huber, T.; Torda, A.; Gunsteren, W. Local elevation: A method for improving the searching properties of molecular dynamics simulation J. Comput.-Aided Mol. Des. 1994, 8, 695-708
22. Kumar, S.; Rosenberg, J. M.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A. The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method J. Comput. Chem. 1992, 13, 1011-1021
23. Grossfield, A. WHAM: the Weighted Histogram Analysis Method 2.0.7; Grossfield Lab: Rochester, NY, 2013.
24. Case, D. A.; Darden, T. A.; Cheatham, T. E.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Walker, R. C.; Zhang, W.; Merz, K. M.; Roberts, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Swails, J.; Goetz, A. W.; Kolossváry, I.; Wong, K. F.; Paesani, F.; Vanicek, J.; Wolf, R. M.; Liu, J.; Wu, X.; Brozell, S. R.; Steinbrecher, T.; Gohlke, H.; Cai, Q.; Ye, X.; Wang, J.; Hsieh, M. J.; Cui, G.; Roe, D. R.; Mathews, D. H.; Seetin, M. G.; Salomon-Ferrer, R.; Sagui, C.; Babin, V.; Luchko, T.; Gusarov, S.; Kovalenko, A.; Kollman, P. A. Amber12; University of California: San Francisco, CA, 2012.
25. Metropolis, N.; Rosenbluth, A. W.; Rosenbluth, M. N.; Teller, A. H.; Teller, E. Equation of State Calculations by Fast Computing Machines J. Chem. Phys. 1953, 21, 1087-1092
26. Pérez, A.; Marchán, I.; Svozil, D.; Sponer, J., III; Laughton, C. A.; Orozco, M. Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers Biophys. J. 2007, 92, 3817-3829
27. Laughton, C. A.; Tanious, F.; Nunn, C. M.; Boykin, D. W.; Wilson, W. D.; Neidle, S. A Crystallographic and Spectroscopic Study of the Complex between d(CGCGAATTCGCG)2 and 2,5-Bis(4-guanylphenyl)furan, an Analogue of Berenil. Structural Origins of Enhanced DNA-Binding Affinity Biochemistry 1996, 35, 5655-5661
28. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 1983, 79, 926-935
29. Joung, I. S.; Cheatham, T. E. Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations J. Phys. Chem. B 2008, 112, 9020-9041
30. Mazur, S.; Tanious, F. A.; Ding, D.; Kumar, A.; Boykin, D. W.; Simpson, I. J.; Neidle, S.; Wilson, W. D. A thermodynamic and structural analysis of DNA minor-groove complex formation J. Mol. Biol. 2000, 300, 321-337