The SAMPL4 hydration challenge: Evaluation of partial charge sets with explicit-water molecular dynamics simulations

Journal of Computer-Aided Molecular Design

Volumn 28, Issue 3, 2014, Pages 277-287

  Muddana, Hari S ^a   Sapra, Neil V ^a   Fenley, Andrew T ^a   Gilson, Michael K ^a  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

AM1 BCC; Hydration; IPolQ; Partial charge; RESP; SAMPL4; VCharge

Indexed keywords

FREE ENERGY; MOLECULAR DYNAMICS;

AM1-BCC; DYNAMICS SIMULATION; ELECTROSTATIC POTENTIALS; EXPLICIT WATER; IPOLQ; PARTIAL CHARGE MODELS; PARTIAL CHARGES; RESTRAINED ELECTROSTATIC POTENTIAL; SAMPL4; VCHARGE;

HYDRATION;

NITRIC ACID DERIVATIVE; SOLVENT; TERTIARY AMINE; WATER;

ACCURACY; ANALYTIC METHOD; ARTICLE; CHEMICAL MODEL; COMPARATIVE STUDY; CONTROLLED STUDY; ENERGY; FORCE; HYDRATION; MOLECULAR DYNAMICS; PRIORITY JOURNAL; SIMULATION; STATIC ELECTRICITY; CHEMISTRY; THERMODYNAMICS;

MODELS, CHEMICAL; MOLECULAR DYNAMICS SIMULATION; STATIC ELECTRICITY; THERMODYNAMICS; WATER;

EID: 84899972979     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-014-9714-6     Document Type: Article

References (55)

1. Levy Y, Onuchic JN (2006) Water mediation in protein folding and molecular recognition. Annu Rev Bioph Biom 35:389-415 (Pubitemid 43877384)
2. Kauzmann W (1959) Some factors in the interpretation of protein denaturation. Adv Protein Chem 14:1-63
3. Tanford C (1962) Contribution of hydrophobic interactions to stability of globular conformation of proteins. J Am Chem Soc 84(22):4240
4. Lockhart DJ, Kim PS (1993) Electrostatic screening of charge and dipole interactions with the helix backbone. Science 260(5105):198-202
5. Tan CH, Yang LJ, Luo R (2006) How well does Poisson-Boltzmann implicit solvent agree with explicit solvent? A quantitative analysis. J Phys Chem B 110(37):18680-18687 (Pubitemid 44547378)
6. Ladbury JE (1996) Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design. Chem Biol 3(12):973-980
7. Nicholls A, Honig B (1991) A rapid finite-difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation. J Comput Chem 12(4):435-445
8. Gilson MK, Sharp KA, Honig BH (1988) Calculating the electrostatic potential of molecules in solution - method and error assessment. J Comput Chem 9(4):327-335
9. Im W, Beglov D, Roux B (1998) Continuum solvation model: computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation. Comput Phys Commun 111(1-3):59-75 (Pubitemid 128400465)
10. Still WC, Tempczyk A, Hawley RC, Hendrickson T (1990) Semianalytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc 112(16):6127-6129
11. Onufriev A, Bashford D, Case DA (2000) Modification of the generalized born model suitable for macromolecules. J Phys Chem B 104(15):3712-3720
12. Lee MS, Salsbury FR, Brooks CL (2002) Novel generalized born methods. J Chem Phys 116(24):10606-10614 (Pubitemid 34751160)
13. Sigalov G, Fenley A, Onufriev A (2006) Analytical electrostatics for biomolecules: beyond the generalized Born approximation. J Chem Phys 124(12):124902
14. Gallicchio E, Paris K, Levy RM (2009) The AGBNP2 implicit solvation model. J Chem Theory Comput 5(9):2544-2564
15. Warshel A (1979) Calculations of chemical processes in solutions. J Phys Chem-Us 83(12):1640-1652
16. Kovalenko A, Hirata F (2000) Potentials of mean force of simple ions in ambient aqueous solution. I. Three-dimensional reference interaction sitemodel approach. J Chem Phys 112(23):10391-10402
17. Kovalenko A, Hirata F (2000) Potentials of mean force of simple ions in ambient aqueous solution. II. Solvation structure from the three-dimensional reference interaction site model approach, and comparison with simulations. J Chem Phys 112(23):10403-10417
18. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79(2):926-935
19. Mobley DL, Bayly CI, Cooper MD, Shirts MR, Dill KA (2009) Small molecule hydration free energies in explicit solvent: an extensive test of fixed-charge atomistic simulations. J Chem Theory Comput 5(2):350-358
20. Muddana HS, Gilson MK (2012) Prediction of SAMPL3 host-guest binding affinities: evaluating the accuracy of generalized force-fields. J Comput Aid Mol Des 26(5):517-525
21. Halgren TA (1992) Representation of van der Waals (vdW) interactions in molecular mechanics force-fields - potential form, combination rules, and vdW parameters. J Am Chem Soc 114(20):7827-7843
22. Kaminski GA, Stern HA, Berne BJ, Friesner RA, Cao YXX, Murphy RB, Zhou RH, Halgren TA (2002) Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests. J Comput Chem 23(16):1515-1531 (Pubitemid 35330854)
23. Ponder JW, Wu CJ, Ren PY, Pande VS, Chodera JD, Schnieders MJ, Haque I, Mobley DL, Lambrecht DS, DiStasio RA, Head-Gordon M, Clark GNI, Johnson ME, Head-Gordon T (2010) Current status of the AMOEBA polarizable force field. J Phys Chem B 114(8):2549-2564
24. Mobley DL, Dumont E, 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 (Pubitemid 46447557)
25. Guthrie JP (2009) A blind challenge for computational solvation free energies: introduction and overview. J Phys Chem B 113(14):4501-4507
26. Geballe MT, Skillman AG, Nicholls A, Guthrie JP, Taylor PJ (2010) The SAMPL2 blind prediction challenge: introduction and overview. J Comput Aid Mol Des 24(4):259-279
27. Geballe MT, Guthrie JP (2012) The SAMPL3 blind prediction challenge: transfer energy overview. J Comput Aid Mol Des 26(5):489-496
28. Muddana HS, Varnado CD, Bielawski CW, Urbach AR, Isaacs L, Geballe MT, Gilson MK (2012) Blind prediction of host-guest binding affinities: a new SAMPL3 challenge. J Comput Aid Mol Des 26(5):475-487
29. Mobley DL, Wymer KL, Lim NM (2014) Blind prediction of solvation free energies from the SAMPL4 challenge. J Comput Aid Mol Des 24:357
30. Muddana HS, Fenley AT, Mobley DL, Gilson MK (2014) Blind prediction of the host-guest binding affinities from the SAMPL4 challenge. J Comput Aid Mol Des
31. Staudinger J, Roberts PV (1996) A critical review of Henry's law constants for environmental applications. Crit Rev Environ Sci Tec 26(3):205-297 (Pubitemid 26307214)
32. Saxena P, Hildemann LM (1996) Water-soluble organics in atmospheric particles: a critical review of the literature and application of thermodynamics to identify candidate compounds. J Atmos Chem 24(1):57-109
33. Suntio LR, Shiu WY, Mackay D, Seiber JN, Glotfelty D (1988) Critical-review of Henry Law constants for pesticides. Rev Environ Contam T 103:1-59
34. Wang JM, 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
35. Bayly CI, Cieplak P, Cornell WD, Kollman PA (1993) A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges - the RESP model. J Phys Chem-Us 97(40):10269-10280
36. 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
37. Jakalian A, Jack DB, Bayly CI (2002) Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation. J Comput Chem 23(16):1623-1641 (Pubitemid 35330860)
38. Gilson MK, Gilson HS, Potter MJ (2003) Fast assignment of accurate partial atomic charges: an electronegativity equalization method that accounts for alternate resonance forms. J Chem Inf Comput Sci 43(6):1982-1997
39. Cerutti DS, Rice JE, Swope WC, Case DA (2013) Derivation of fixed partial charges for amino acids accommodating a specific water model and implicit polarization. J Phys Chem B 117(8):2328-2338
40. Karamertzanis PG, Raiteri P, Galindo A (2010) The use of anisotropic potentials in modeling water and free energies of hydration. J Chem Theory Comput 6(5):1590-1607
41. Fennell CJ, Wymer KL, Mobley DL (2014) Polarized alcohol in condensed-phase and its role in small molecule hydration. In preparation
42. Muddana HS, Sapra NV, Fenley AT, Gilson MK (2013) The electrostatic response of water to neutral polar solutes: implications for continuum solvent modeling. J Chem Phys 138(22):224504
43. Beutler TC, Mark AE, Vanschaik 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
44. Bennett CH (1976) Efficient estimation of free-energy differences from Monte-Carlo data. J Comput Phys 22(2):245-268
45. 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
46. Berendsen HJC, Postma JPM, van Gunsteren WF, Dinola A, Haak JR (1984) Molecular-dynamics with coupling to an external bath. J Chem Phys 81(8):3684-3690
47. Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) A smooth particle mesh Ewald method. J Chem Phys 103(19):8577-8593
48. Miyamoto S, Kollman PA (1992) Settle - an analytical version of the Shake and Rattle algorithm for rigid water models. J Comput Chem 13(8):952-962
49. Wang JM, 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 (Pubitemid 44363172)
50. Mennucci B, Cammi R, Tomasi J (1998) Excited states and solvatochromic shifts within a nonequilibrium solvation approach: a new formulation of the integral equation formalism method at the self-consistent field, configuration interaction, and multiconfiguration self-consistent field level. J Chem Phys 109(7):2798-2807 (Pubitemid 128678172)
51. Shivakumar D, Deng YQ, Roux B (2009) Computations of absolute solvation free energies of small molecules using explicit and implicit solvent model. J Chem Theory Comput 5(4):919-930
52. Shivakumar D, Williams J, Wu YJ, Damm W, Shelley J, Sherman W (2010) Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field. J Chem Theory Comput 6(5):1509-1519
53. Jorgensen WL, Maxwell DS, TiradoRives J (1996) Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 118(45):11225-11236 (Pubitemid 26399746)
54. Momany FA, Rone R (1992) Validation of the general-purpose Quanta(R)3.2/Charmm(R) force-field. J Comput Chem 13(7):888-900
55. Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, Darian E, Guvench O, Lopes P, Vorobyov I, MacKerell AD (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