Calculation of binding free energies

Methods in Molecular Biology

Volumn 1215, Issue , 2015, Pages 173-209

  Gapsys, Vytautas ^a   Michielssens, Servaas ^a   Henning Peters, Jan ^a   De Groot, Bert L ^a   Leonov, Hadas ^a  

^a NONE

Author keywords

Alchemical transitions; Crooks Fluctuation Theorem; Free energy; Hybrid topology; Molecular dynamics; Non equilibrium methods; Protein protein interaction; Protein ligand binding

Indexed keywords

ARTICLE; CALCULATION; ENERGY; HYBRID; PRIORITY JOURNAL; PROTEIN BINDING; SOLVATION; THEORETICAL STUDY; THERMODYNAMICS; VALIDATION STUDY;

EID: 84921827868     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-1465-4_9     Document Type: Article

References (71)

1. Torrie GM, Valleau JP (1977) Nonphysical sampling distributions in Monte Carlo free-energy estimation: umbrella sampling. J Comput Phys 23(2):187–199
2. Kirkwood JG (1935) Statistical mechanics of fluid mixtures. J Chem Phys 3:300–313
3. Ben-Naim A (1992) Statistical thermodynamics for chemists and biochemists. Plenum Press, New York
4. Chipot C, Pohorille A (eds) (2007) Free energy calculations. Theory and applications in chemistry and biology. Springer series in chemical physics, vol 86
5. Christ CD, Mark AE, van Gunsteren WF (2010) Basic ingredients of free energy calculations: a review. J Comput Chem 31(8):1569–1582. ISSN 1096-987X. doi:10.1002/jcc.21450. http://dx.doi.org/10.1002/jcc.21450
6. Michael S, David M (2013) An introduction to best practices in free energy calculations. In: Biomolecular simulations: methods and protocols. Methods in molecular biology, vol 924. Humana Press, New York, pp 271–311
7. Zwanzig RW (1954) High-temperature equation of state by a perturbation method. I. Nonpolar gases. J Chem Phys 22: 1420–1426
8. Pohorille A, Jarzynski C, Chipot C (2010) Good practices in free-energy calculations. J Phys Chem B 114(32):10235–10253
9. Landau LD (1938) Statistical physics. The Clarendon Press, Oxford
10. Lu N, Kofke DA (2001) Accuracy of free-energy perturbation calculations in molecular simulation. I. Modeling. J Chem Phys 114: 7303–7311
11. Lu N, Kofke DA (2001) Accuracy of free-energy perturbation calculations in molecular simulation. II. Heuristics. J Chem Phys 115: 6866–6875
12. Shirts MR, Pande VS (2005) Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration. J Chem Phys 122(14):144107-1–144107-16
13. Bennett CH (1976) Efficient estimation of free energy differences from Monte Carlo data. J Comput Phys 22(2):245–268
14. Shirts MR, Bair E, Hooker G, Pande VS (2003) Equilibrium free energies from nonequilibrium measurements using maximum-likelihood methods. Phys Rev Lett 91(14):140601
15. Mezei M (1992) Polynomial path for the calculation of liquid state free energies from computer simulations tested on liquid water. J Comput Chem 13(5):651–656
16. Steinbrecher T, Mobley DL, Case DA (2007) Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations. J Chem Phys 127:214108
17. Kumar S, Rosenberg JM, Bouzida D, Swendsen RH, Kollman PA (1992) The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. J Comput Chem 13(8):1011–1021
18. Shirts MR, Chodera JD (2008) Statistically optimal analysis of samples from multiple equilibrium states. J Chem Phys 129:124105
19. Shenfeld DK, Xu H, Eastwood MP, Dror RO, Shaw DE (2009) Minimizing thermodynamic length to select intermediate states for free-energy calculations and replica-exchange simulations. Phys Rev E 80(4):046705
20. Buelens FP, Grubmüller H (2012) Linear-scaling soft-core scheme for alchemical free energy calculations. J Comput Chem 33(1): 25–33
21. Mazor M, Pettitt BM (1991) Convergence of the chemical potential in aqueous simulations. Mol Simul 6(1–3):1–4
22. Mitchell MJ, McCammon JA (1991) Free energy difference calculations by thermodynamic integration: difficulties in obtaining a precise value. J Comput Chem 12(2):271–275
23. Straatsma TP, McCammon JA (1991) Multiconfiguration thermodynamic integration. J Chem Phys 95:1175
24. Jorge M, Garrido NM, Queimada AJ, Economou IG, Macedo EA (2010) Effect of the integration method on the accuracy and computational efficiency of free energy calculations using thermodynamic integration. J Chem Theory Comput 6(4):1018–1027
25. Bruckner S, Boresch S (2011) Efficiency of alchemical free energy simulations. II. Improvements for thermodynamic integration. J Comput Chem 32(7):1320–1333
26. Jarzynski C (1997) Nonequilibrium equality for free energy differences. Phys Rev Lett 78(14):2690–2693
27. Cuendet MA (2006) The Jarzynski identity derived from general hamiltonian or non-hamiltonian dynamics reproducing NVT or NPT ensembles. J Chem Phys 125:144109
28. Hummer G (2001) Fast-growth thermodynamic integration: error and efficiency analysis. J Chem Phys 114:7330–7337
29. Gore J, Ritort F, Bustamante C (2003) Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurements. Proc Natl Acad Sci USA 100(22): 12564–12569
30. Crooks GE (1998) Nonequilibrium measurements of free energy differences for microscopically reversible Markovian systems. J Stat Phys 90(5–6):1481–1487
31. Crooks GE (1999) Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences. Phys Rev E 60(3):2721–2726
32. Chelli R, Marsili S, Barducci A, Procacci P (2007) Recovering the Crooks equation for dynamical systems in the isothermal-isobaric ensemble: a strategy based on the equations of motion. J Chem Phys 126:044502
33. Nanda H, Lu N, Woolf TB (2005) Using non-Gaussian density functional fits to improve relative free energy calculations. J Chem Phys 122(13):134110-1–134110-8
34. Maragakis P, Ritort F, Bustamante C, Karplus M, Crooks GE (2008) Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise. J Chem Phys 129:024102
35. Goette M, Grubmüller H (2009) Accuracy and convergence of free energy differences calculated from nonequilibrium switching processes. J Comput Chem 30(3):447–456
36. Bramwell ST, Christensen K, Fortin J-Y, Holdsworth PCW, Jensen HJ, Lise S, López JM, Nicodemi M, Pinton J-F, Sellitto M (2000) Universal fluctuations in correlated systems. Phys Rev Lett 84(17):3744–3747
37. Massey FJ Jr (1951) The Kolmogorov-Smirnov test for goodness of fit. J Am Stat Assoc 46(253):68–78
38. Pearlman DA, Kollman PA (1991) The overlooked bond-stretching contribution in free energy perturbation calculations. J Chem Phys 94:4532-4545
39. Pearlman DA (1994) A comparison of alternative approaches to free energy calculations. J Phys Chem 98(5):1487–1493
40. Boresch S, Karplus M (1999) The role of bonded terms in free energy simulations. 2. Calculation of their influence on free energy differences of solvation. J Phys Chem A 103(1):119–136
41. Boresch S, Karplus M (1999) The role of bonded terms in free energy simulations: 1. Theoretical analysis. J Phys Chem A 103(1): 103–118
42. Bash PA, Singh UC, Langridge R, Kollman PA (1987) Free energy calculations by computer simulation. Science 236(4801):564–568
43. Beutler TC, Mark AE, van Schaik RC, Gerber PR, van Gunsteren WF (1994) Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations. Chem Phys Lett 222(6):529–539. ISSN 0009-2614
44. Zacharias M, Straatsma TP, McCammon JA (1994) Separation-shifted scaling, a new scaling method for Lennard-Jones interactions in thermodynamic integration. J Chem Phys 100: 9025–9031
45. Gapsys V, Seeliger D, de Groot BL (2012) New soft-core potential function for molecular dynamics based alchemical free energy calculations. J Chem Theory Comput 8(7): 2373–2382
46. Tosco P, Balle T, Shiri F (2011) Open 3DALIGN: an open-source software aimed at unsupervised ligand alignment. J Comput Aided Mol Des 25(8):777–783
47. Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4(3): 435–447
48. Seeliger D, De Groot BL (2010) Protein thermostability calculations using alchemical free energy simulations. Biophys J 98(10):2309–2316. ISSN 0006-3495
49. O’Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR (2011) Open Babel: an open chemical toolbox. J Cheminf 3(1):1–14
50. Sadowski J, Gasteiger J, Klebe G (1994) Comparison of automatic three-dimensional model builders using 639 X-ray structures. J Chem Inf Comput Sci 34(4):1000–1008
51. Singh UC, Kollman PA (1984) An approach to computing electrostatic charges for molecules. J Comput Chem 5(2):129–145
52. Bayly CI, Cieplak P, Cornell W, Kollman PA (1993) A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. J Phys Chem 97(40):10269–10280
53. Jakalian A, Bush BL, Jack DB, Bayly CI (2000) Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method. J Comput Chem 21(2):132–146
54. Mobley DL, Dumont É, Chodera JD, Dill KA (2007) Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent. J Phys Chem B 111(9):2242–2254
55. Wang J, Wang W, Kollman PA, Case DA (2006) Automatic atom type and bond type perception in molecular mechanical calculations. J Mol Graph Model 25(2):247–260
56. Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) Development and testing of a general amber force field. J Comput Chem 25(9):1157–1174
57. Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, Darian E, Guvench O, Lopes P, Vorobyov I, MacKerell AD Jr (2010) CHARMM general force field: a force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J Comput Chem 31(4):671–690
58. Vanommeslaeghe K, MacKerell AD Jr (2012) Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing. J Chem Inf Model 52(12): 3144–3154
59. Vanommeslaeghe K, Raman EP, MacKerell AD Jr (2012) Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges. J Chem Inf Model 52(12):3155–3168
60. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE (2011) An automated force field topology builder (ATB) and repository: version 1.0. J Chem Theory Comput 7(12):4026–4037
61. Ribeiro AAST, Horta BAC, de Alencastro RB (2008) MKTOP: a program for automatic construction of molecular topologies. J Braz Chem Soc 19(7):1433–1435
62. Rocklin GJ, Mobley DL, Dill KA, Hünenberger PH (2013) Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice sum methods: an accurate correction scheme for electrostatic finite-size effects. J Chem Phys 139(18):184103.
63. Talhout R, Villa A, Mark AE, Engberts JBFN (2003) Understanding binding affinity: a combined isothermal titration calorimetry/ molecular dynamics study of the binding of aseries of hydrophobically modified benzamidinium chloride inhibitors to trypsin. J Am Chem Soc 125(35):10570–10579
64. Marquart M, Walter J, Deisenhofer J, Bode W, Huber R (1983) The geometry of the reactive site and of the peptide groups in trypsin, trypsinogen and its complexes with inhibitors. Acta Crystallogr Sect B Struct Sci 39(4):480–490
65. Lu W, Apostol I, Qasim MA, Warne N, Wynn R, Zhang WL, Anderson S, Chiang YW, Ogin E, Rothberg I, Ryan K, Laskowski M (1997) Binding of amino acid side-chains to S1 cavities of serine proteinases. J Mol Biol 266(2): 441–461
66. Benedix A, Becker CM, de Groot BL, Caflisch A, Böckmann RA (2009) Predicting free energy changes using structural ensembles. Nat Methods 6(1):3–4
67. Fujinaga M, Sielecki AR, Read RJ, Ardelt W, Laskowski M, James MNG (1987) Crystal and molecular structures of the complex of α-chymotrypsin with its inhibitor turkey ovomucoid third domain at 1.8 Å resolution. J Mol Biol 195(2):397–418
68. Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C (2006) Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins Struct Funct Bioinform 65(3): 712–725
69. Mobley DL, Chodera JD, Dill KA (2006) On the use of orientational restraints and symmetry corrections in alchemical free energy calculations. J Chem Phys 125(8):084902. doi: 10.1063/1.2221683. http://link.aip.org/link/?JCP/125/084902/1
70. Shirts MR, Pitera JW, Swope WC, Pande VS (2003) Extremely precise free energy calculations of amino acid side chain analogs: comparison of common molecular mechanics force fields for proteins. J Chem Phys 119(11): 5740–5761
71. Shirts MR, Mobley DL, Chodera JD, Pande VS (2007) Accurate and efficient corrections for missing dispersion interactions in molecular simulations. J Phys Chem B 111(45): 13052–13063