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Volumn 4, Issue 1, 2014, Pages 71-89

Frontiers in free-energy calculations of biological systems

Author keywords

[No Author keywords available]

Indexed keywords

MACHINERY; MATHEMATICAL TRANSFORMATIONS; MOLECULAR DYNAMICS;

EID: 84890794190     PISSN: 17590876     EISSN: 17590884     Source Type: Journal    
DOI: 10.1002/wcms.1157     Document Type: Review
Times cited : (152)

References (122)
  • 2
    • 34548717559 scopus 로고
    • Phase transition for a hard sphere systems
    • Alder BJ, Wainwright TE. Phase transition for a hard sphere systems. J Chem Phys 1957, 27:1208-1209.
    • (1957) J Chem Phys , vol.27 , pp. 1208-1209
    • Alder, B.J.1    Wainwright, T.E.2
  • 6
    • 33646987405 scopus 로고
    • Optimized Monte Carlo data analysis
    • Ferrenberg AM, Swendsen RH. Optimized Monte Carlo data analysis. Phys Rev Lett 1989, 63:1195-1198.
    • (1989) Phys Rev Lett , vol.63 , pp. 1195-1198
    • Ferrenberg, A.M.1    Swendsen, R.H.2
  • 7
    • 84986519238 scopus 로고
    • The weighted histogram analysis method for free energy calculations on biomolecules. I. The method
    • Kumar S, Bouzida D, Swendsen RH, Kollman PA, Rosenberg JM. The weighted histogram analysis method for free energy calculations on biomolecules. I. The method. J Comput Chem 1992, 13:1011-1021.
    • (1992) J Comput Chem , vol.13 , pp. 1011-1021
    • Kumar, S.1    Bouzida, D.2    Swendsen, R.H.3    Kollman, P.A.4    Rosenberg, J.M.5
  • 9
    • 36849122972 scopus 로고
    • High-temperature equation of state by a perturbation method. I. Nonpolar gases
    • Zwanzig RW. High-temperature equation of state by a perturbation method. I. Nonpolar gases. J Chem Phys 1954, 22:1420-1426.
    • (1954) J Chem Phys , vol.22 , pp. 1420-1426
    • Zwanzig, R.W.1
  • 10
    • 4243754128 scopus 로고    scopus 로고
    • Nonequilibrium equality for free energy differences
    • Jarzynski C. Nonequilibrium equality for free energy differences. Phys Rev Lett 1997, 78:2690-2693.
    • (1997) Phys Rev Lett , vol.78 , pp. 2690-2693
    • Jarzynski, C.1
  • 11
    • 33646471468 scopus 로고
    • Statistical mechanics of fluid mixtures
    • Kirkwood JG. Statistical mechanics of fluid mixtures. J Chem Phys 1935, 3:300-313.
    • (1935) J Chem Phys , vol.3 , pp. 300-313
    • Kirkwood, J.G.1
  • 13
    • 34247626293 scopus 로고    scopus 로고
    • Partitioning of amino acid side chains into lipid bilayers: results from computer simulations and comparison to experiment
    • MacCallum JL, Bennett WFD, Tieleman DP. Partitioning of amino acid side chains into lipid bilayers: results from computer simulations and comparison to experiment. J Gen Physiol 2007, 129:371-377.
    • (2007) J Gen Physiol , vol.129 , pp. 371-377
    • MacCallum, J.L.1    Bennett, W.F.D.2    Tieleman, D.P.3
  • 14
    • 39749132236 scopus 로고    scopus 로고
    • Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations
    • Johansson ACV, Lindahl E. Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations. Proteins 2008, 70:1332-1344.
    • (2008) Proteins , vol.70 , pp. 1332-1344
    • Johansson, A.C.V.1    Lindahl, E.2
  • 15
    • 34247633528 scopus 로고    scopus 로고
    • On the thermodynamic stability of a charged arginine side chain in a transmembrane helix
    • Dorairaj S, Allen TW. On the thermodynamic stability of a charged arginine side chain in a transmembrane helix. Proc Natl Acad Sci USA 2007, 104:4943-4948.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 4943-4948
    • Dorairaj, S.1    Allen, T.W.2
  • 16
    • 79952771298 scopus 로고    scopus 로고
    • Free-energy cost for translocon-assisted insertion of membrane proteins
    • Gumbart JC, Chipot C, Schulten K. Free-energy cost for translocon-assisted insertion of membrane proteins. Proc Natl Acad Sci USA 2011, 108:3596-3601.
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 3596-3601
    • Gumbart, J.C.1    Chipot, C.2    Schulten, K.3
  • 17
  • 18
    • 0004504539 scopus 로고
    • Monte Carlo simulation of differences in free energies of hydration
    • Jorgensen WL, Ravimohan C. Monte Carlo simulation of differences in free energies of hydration. J Chem Phys 1985, 83:3050-3054.
    • (1985) J Chem Phys , vol.83 , pp. 3050-3054
    • Jorgensen, W.L.1    Ravimohan, C.2
  • 19
    • 0024365336 scopus 로고
    • Hidden thermodynamics of mutant proteins: a molecular dynamics analysis
    • Gao J, Kuczera K, Tidor B, Karplus M. Hidden thermodynamics of mutant proteins: a molecular dynamics analysis. Science 1989, 244:1069-1072.
    • (1989) Science , vol.244 , pp. 1069-1072
    • Gao, J.1    Kuczera, K.2    Tidor, B.3    Karplus, M.4
  • 21
    • 84855710487 scopus 로고    scopus 로고
    • Constant pH molecular dynamics simulations of nucleic acids in explicit solvent
    • Goh GB, Knight JL, Brooks III, CL. Constant pH molecular dynamics simulations of nucleic acids in explicit solvent. J Chem Theory Comput 2012, 8:36-46.
    • (2012) J Chem Theory Comput , vol.8 , pp. 36-46
    • Goh, G.B.1    Knight, J.L.2    III Brooks, C.L.3
  • 22
    • 0002531265 scopus 로고
    • Methods for calculation of free energies and binding constants: successes and problems
    • van Van Gunsteren, WF, Weiner, PK, eds. The Netherlands: Escom;
    • van Gunsteren WF. Methods for calculation of free energies and binding constants: successes and problems. In: Van Gunsteren, WF, Weiner, PK, eds. Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications. The Netherlands: Escom; 1989, 27-59.
    • (1989) Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications , pp. 27-59
    • Gunsteren, W.F.1
  • 23
    • 0009590921 scopus 로고
    • Free-energy calculations: a breakthrough for modeling organic chemistry in solutions
    • Jorgensen WL. Free-energy calculations: a breakthrough for modeling organic chemistry in solutions. Acc Chem Res 1989, 22:184-189.
    • (1989) Acc Chem Res , vol.22 , pp. 184-189
    • Jorgensen, W.L.1
  • 25
    • 0141990949 scopus 로고    scopus 로고
    • Extremely precise free energy calculations of amino acid chain analogs: comparison of common molecular mechanical force fields for proteins
    • Shirts M, Pitera J, Swope W, Pande V. Extremely precise free energy calculations of amino acid chain analogs: comparison of common molecular mechanical force fields for proteins. J Chem Phys 2003, 119:5740-5761.
    • (2003) J Chem Phys , vol.119 , pp. 5740-5761
    • Shirts, M.1    Pitera, J.2    Swope, W.3    Pande, V.4
  • 26
    • 4444282928 scopus 로고    scopus 로고
    • A biomolecular force field based on the free enthalpy of hydration and solvation: the Gromos force-field parameter sets 53A5 and 53A6
    • Oostenbrink C, Villa A, Mark AE, van Gunsteren WF. A biomolecular force field based on the free enthalpy of hydration and solvation: the Gromos force-field parameter sets 53A5 and 53A6. J Comput Chem 2004, 25:1656-1676.
    • (2004) J Comput Chem , vol.25 , pp. 1656-1676
    • Oostenbrink, C.1    Villa, A.2    Mark, A.E.3    van Gunsteren, W.F.4
  • 27
    • 85005687495 scopus 로고
    • The free energy of xenon binding to myoglobin from molecular-dynamics simulation
    • Hermans J, Shankar S. The free energy of xenon binding to myoglobin from molecular-dynamics simulation. Isr J Chem 1986, 27:225-227.
    • (1986) Isr J Chem , vol.27 , pp. 225-227
    • Hermans, J.1    Shankar, S.2
  • 28
    • 0027239578 scopus 로고
    • What determines the strength of noncovalent association of ligands to proteins in aqueous solution ?
    • Miyamoto S, Kollman PA. What determines the strength of noncovalent association of ligands to proteins in aqueous solution ? Proc Natl Acad Sci USA 1993, 90:8402-8406.
    • (1993) Proc Natl Acad Sci USA , vol.90 , pp. 8402-8406
    • Miyamoto, S.1    Kollman, P.A.2
  • 29
    • 0001382020 scopus 로고    scopus 로고
    • Calculation of absolute binding free energies for charged ligands and effects of long-range electrostatic interactions
    • Åqvist, J. Calculation of absolute binding free energies for charged ligands and effects of long-range electrostatic interactions. J Comput Chem 1996, 17:1587-1597.
    • (1996) J Comput Chem , vol.17 , pp. 1587-1597
    • Åqvist, J.1
  • 30
    • 0023106632 scopus 로고
    • Calculation of the relative change in binding free energy of a protein-inhibitor complex
    • Bash PA, Singh UC, Brown FK, Langridge R, Kollman PA. Calculation of the relative change in binding free energy of a protein-inhibitor complex. Science 1987, 235:574-576.
    • (1987) Science , vol.235 , pp. 574-576
    • Bash, P.A.1    Singh, U.C.2    Brown, F.K.3    Langridge, R.4    Kollman, P.A.5
  • 31
    • 0008796956 scopus 로고
    • Molecular dynamics/free energy perturbation study on the relative affinities of the binding of reduced and oxidized NADP to dihydrofolate reductase
    • Cummins PL, Ramnarayan K, Singh UC, Gready JE. Molecular dynamics/free energy perturbation study on the relative affinities of the binding of reduced and oxidized NADP to dihydrofolate reductase. J Am Chem Soc 1991, 113:8247-8256.
    • (1991) J Am Chem Soc , vol.113 , pp. 8247-8256
    • Cummins, P.L.1    Ramnarayan, K.2    Singh, U.C.3    Gready, J.E.4
  • 32
    • 0025720738 scopus 로고
    • Relative differences in the binding free energies of human immunodeficiency virus 1 protease inhibitors: a thermodynamic cycle-perturbation approach
    • Reddy MR, Viswanadhan VN, Weinstein JN. Relative differences in the binding free energies of human immunodeficiency virus 1 protease inhibitors: a thermodynamic cycle-perturbation approach. Proc Natl Acad Sci USA 1991, 88:10287-10291.
    • (1991) Proc Natl Acad Sci USA , vol.88 , pp. 10287-10291
    • Reddy, M.R.1    Viswanadhan, V.N.2    Weinstein, J.N.3
  • 33
    • 0026641163 scopus 로고
    • Thermodynamics of protein-peptide binding in the Ribonuclease S system studied by molecular dynamics and free energy calculations
    • Simonson T, Brünger, AT. Thermodynamics of protein-peptide binding in the Ribonuclease S system studied by molecular dynamics and free energy calculations. Biochemistry 1992, 31:8661-8674.
    • (1992) Biochemistry , vol.31 , pp. 8661-8674
    • Simonson, T.1    Brünger, A.T.2
  • 34
    • 0030134642 scopus 로고    scopus 로고
    • Estimating the relative free energy of different molecular states with respect to a single reference state
    • van
    • Liu H, Mark AE, van Gunsteren WF. Estimating the relative free energy of different molecular states with respect to a single reference state. J Phys Chem 1996, 100:9485-9494.
    • (1996) J Phys Chem , vol.100 , pp. 9485-9494
    • Liu, H.1    Mark, A.E.2    Gunsteren, W.F.3
  • 35
    • 77955577540 scopus 로고    scopus 로고
    • Good practices in free-energy calculations
    • Pohorille A, Jarzynski C, Chipot C. Good practices in free-energy calculations. J Phys Chem B 2010, 114:10235-10253.
    • (2010) J Phys Chem B , vol.114 , pp. 10235-10253
    • Pohorille, A.1    Jarzynski, C.2    Chipot, C.3
  • 36
    • 0032173123 scopus 로고    scopus 로고
    • Precision and accuracy of staged free-energy perturbation methods for computing the chemical potential by molecular simulation
    • Kofke DA, Cummings PT. Precision and accuracy of staged free-energy perturbation methods for computing the chemical potential by molecular simulation. Fluid Phase Equil 1998, 150:41-49.
    • (1998) Fluid Phase Equil , vol.150 , pp. 41-49
    • Kofke, D.A.1    Cummings, P.T.2
  • 37
    • 5244304444 scopus 로고
    • Efficient estimation of free energy differences from Monte Carlo data
    • Bennett CH. Efficient estimation of free energy differences from Monte Carlo data. J Comp Phys 1976, 22:245-268.
    • (1976) J Comp Phys , vol.22 , pp. 245-268
    • Bennett, C.H.1
  • 38
    • 36849116054 scopus 로고
    • Machine calculation of thermodynamic properties of a simple fluid at supercritical temperatures
    • McDonald IR, Singer K. Machine calculation of thermodynamic properties of a simple fluid at supercritical temperatures. J Chem Phys 1967, 47:4766-4772.
    • (1967) J Chem Phys , vol.47 , pp. 4766-4772
    • McDonald, I.R.1    Singer, K.2
  • 39
    • 0345763766 scopus 로고    scopus 로고
    • Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods
    • Lu N, Kofke DA, Woolf TB. Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods. J Comput Chem 2004, 25:28-39.
    • (2004) J Comput Chem , vol.25 , pp. 28-39
    • Lu, N.1    Kofke, D.A.2    Woolf, T.B.3
  • 40
    • 52949088587 scopus 로고    scopus 로고
    • Statistically optimal analysis of samples from multiple equilibrium states
    • Shirts MR, Chodera JD. Statistically optimal analysis of samples from multiple equilibrium states. J Chem Phys 2008, 129:124105.
    • (2008) J Chem Phys , vol.129 , pp. 124105
    • Shirts, M.R.1    Chodera, J.D.2
  • 41
    • 36849102835 scopus 로고
    • Monte Carlo estimation of the free energy by multistage sampling
    • Valleau JP, Card DN. Monte Carlo estimation of the free energy by multistage sampling. J Chem Phys 1972, 57:5457-5462.
    • (1972) J Chem Phys , vol.57 , pp. 5457-5462
    • Valleau, J.P.1    Card, D.N.2
  • 42
    • 21544442740 scopus 로고
    • Computer-simulation study of free-energy barriers in crystal nucleation
    • van
    • van Duijneveldt S, Frenkel D. Computer-simulation study of free-energy barriers in crystal nucleation. J Chem Phys 1992, 96:4655-4668.
    • (1992) J Chem Phys , vol.96 , pp. 4655-4668
    • Duijneveldt, S.1    Frenkel, D.2
  • 43
    • 0001927585 scopus 로고
    • On information and sufficiency
    • Kullback S, Leibler R. On information and sufficiency. Ann Math Stat 1951, 22:79-86.
    • (1951) Ann Math Stat , vol.22 , pp. 79-86
    • Kullback, S.1    Leibler, R.2
  • 44
    • 0042640726 scopus 로고
    • Some topics in the theory of fluids
    • Widom B. Some topics in the theory of fluids. J Chem Phys 1963, 39:2808-2812.
    • (1963) J Chem Phys , vol.39 , pp. 2808-2812
    • Widom, B.1
  • 45
    • 0000249851 scopus 로고
    • Avoiding singularities and neumerical instabilities in free energy calculations based on molecular simulations
    • Beutler TC, Mark AE, van Schaik RC, Gerber PR, van Gunsteren WF. Avoiding singularities and neumerical instabilities in free energy calculations based on molecular simulations. Chem Phys Lett 1994, 222:529-539.
    • (1994) Chem Phys Lett , vol.222 , pp. 529-539
    • Beutler, T.C.1    Mark, A.E.2    van Schaik, R.C.3    Gerber, P.R.4    van Gunsteren, W.F.5
  • 46
    • 36449002336 scopus 로고
    • Separation-shifted scaling, a new scaling method for Lennard-Jones interactions in thermodynamic integration
    • Zacharias M, Straatsma TP, McCammon, JA. Separation-shifted scaling, a new scaling method for Lennard-Jones interactions in thermodynamic integration. J Chem Phys 1994, 100:9025-9031.
    • (1994) J Chem Phys , vol.100 , pp. 9025-9031
    • Zacharias, M.1    Straatsma, T.P.2    McCammon, J.A.3
  • 47
    • 0025319621 scopus 로고
    • Calculation of the relative binding free energy of 2'GMP and 2'AMP to ribonuclease T1 using molecular dynamics/free energy perturbation approaches
    • Hirono S, Kollman PA. Calculation of the relative binding free energy of 2'GMP and 2'AMP to ribonuclease T1 using molecular dynamics/free energy perturbation approaches. J Mol Biol 1990, 212:197-209.
    • (1990) J Mol Biol , vol.212 , pp. 197-209
    • Hirono, S.1    Kollman, P.A.2
  • 48
    • 0000318631 scopus 로고
    • Calculation of relative free energy via indirect pathways
    • Mark AE, van Gunsteren WF, Berendsen HJC. Calculation of relative free energy via indirect pathways. J Chem Phys 1991, 91:3808-3816.
    • (1991) J Chem Phys , vol.91 , pp. 3808-3816
    • Mark, A.E.1    van Gunsteren, W.F.2    Berendsen, H.J.C.3
  • 49
    • 0141956086 scopus 로고    scopus 로고
    • Single-step perturbations to calculate free energy differences from unphysical reference states: limits on size, flexibility, and character
    • Oostenbrink C, van Gunsteren WF. Single-step perturbations to calculate free energy differences from unphysical reference states: limits on size, flexibility, and character. J Comput Chem 2003, 24:1730-1739.
    • (2003) J Comput Chem , vol.24 , pp. 1730-1739
    • Oostenbrink, C.1    van Gunsteren, W.F.2
  • 50
    • 34248388140 scopus 로고    scopus 로고
    • Enveloping distribution sampling: a method to calculate free energy differences from a single simulation
    • Christ CD, van Gunsteren WF. Enveloping distribution sampling: a method to calculate free energy differences from a single simulation. J Chem Phys 2007, 126:184110.
    • (2007) J Chem Phys , vol.126 , pp. 184110
    • Christ, C.D.1    van Gunsteren, W.F.2
  • 51
    • 44049091290 scopus 로고    scopus 로고
    • Calculation of protein-ligand binding free energy by using a polarizable potential
    • Jiao D, Golubkov PA, Darden TA, Ren P. Calculation of protein-ligand binding free energy by using a polarizable potential. Proc Natl Acad Sci USA 2008, 105:6290-6295.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 6290-6295
    • Jiao, D.1    Golubkov, P.A.2    Darden, T.A.3    Ren, P.4
  • 52
    • 36549092795 scopus 로고
    • Efficient computation of absolute free energies of binding by computer simulations. Application to the methane dimer in water
    • Jorgensen WL, Buckner JK, Boudon S, Tirado-Rives J. Efficient computation of absolute free energies of binding by computer simulations. Application to the methane dimer in water. J Chem Phys 1988, 89:3742-3746.
    • (1988) J Chem Phys , vol.89 , pp. 3742-3746
    • Jorgensen, W.L.1    Buckner, J.K.2    Boudon, S.3    Tirado-Rives, J.4
  • 53
    • 0141682863 scopus 로고    scopus 로고
    • Absolute binding free energies: a quantitative approach to their calculation
    • Boresch S, Tettinger F, Leitgeb M, Karplus M. Absolute binding free energies: a quantitative approach to their calculation. J Phys Chem B 2003, 107:9535-9551.
    • (2003) J Phys Chem B , vol.107 , pp. 9535-9551
    • Boresch, S.1    Tettinger, F.2    Leitgeb, M.3    Karplus, M.4
  • 55
    • 33749238080 scopus 로고    scopus 로고
    • Calculation of standard binding free energies: aromatic molecules in the T4 lysozyme L99A mutant
    • Deng Y, Roux B. Calculation of standard binding free energies: aromatic molecules in the T4 lysozyme L99A mutant. J Chem Theor Comp 2006, 2:1255-1273.
    • (2006) J Chem Theor Comp , vol.2 , pp. 1255-1273
    • Deng, Y.1    Roux, B.2
  • 56
    • 54849417403 scopus 로고    scopus 로고
    • Calculation of absolute protein-ligand binding free energy using distributed replica sampling
    • Rodinger T, Howell PL, Pomès, R. Calculation of absolute protein-ligand binding free energy using distributed replica sampling. J Chem Phys 2008, 129:155102.
    • (2008) J Chem Phys , vol.129 , pp. 155102
    • Rodinger, T.1    Howell, P.L.2    Pomès, R.3
  • 57
    • 70449522914 scopus 로고    scopus 로고
    • Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site
    • Boyce SE, Mobley DL, Rocklin GJ, Graves AP, Dill KA, Shoichet BK. Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site. J Mol Biol 2009, 394:747-763.
    • (2009) J Mol Biol , vol.394 , pp. 747-763
    • Boyce, S.E.1    Mobley, D.L.2    Rocklin, G.J.3    Graves, A.P.4    Dill, K.A.5    Shoichet, B.K.6
  • 58
    • 73949121918 scopus 로고    scopus 로고
    • Computation of absolute hydration and binding free energy with free energy perturbation distributed replica-exchange molecular dynamics
    • Jiang W, Hodoscek M, Roux B. Computation of absolute hydration and binding free energy with free energy perturbation distributed replica-exchange molecular dynamics. J Chem Theory Comput 2009, 5:2583-2588.
    • (2009) J Chem Theory Comput , vol.5 , pp. 2583-2588
    • Jiang, W.1    Hodoscek, M.2    Roux, B.3
  • 59
    • 78651242089 scopus 로고    scopus 로고
    • New method for calculating the absolute free energy of binding: the effect of a mobile loop on the avidin/biotin complex
    • General IJ, Dragomirova R, Meirovitch H. New method for calculating the absolute free energy of binding: the effect of a mobile loop on the avidin/biotin complex. J Phys Chem B 2011, 115:168-175.
    • (2011) J Phys Chem B , vol.115 , pp. 168-175
    • General, I.J.1    Dragomirova, R.2    Meirovitch, H.3
  • 60
    • 0021582448 scopus 로고
    • Ligand-receptor interactions
    • Tembe BL, McCammon, JA. Ligand-receptor interactions. Comp Chem 1984, 8:281-283.
    • (1984) Comp Chem , vol.8 , pp. 281-283
    • Tembe, B.L.1    McCammon, J.A.2
  • 61
    • 0036286654 scopus 로고    scopus 로고
    • Free energy simulations come of age: protein-ligand recognition
    • Simonson T, Archontis G, Karplus M. Free energy simulations come of age: protein-ligand recognition. Acc Chem Res 2002, 35:430-437.
    • (2002) Acc Chem Res , vol.35 , pp. 430-437
    • Simonson, T.1    Archontis, G.2    Karplus, M.3
  • 65
    • 84875365986 scopus 로고    scopus 로고
    • Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes
    • Knight JL, Yesselman JD, Brooks, CL III. Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes. J Comput Chem 2013, 34:893-903.
    • (2013) J Comput Chem , vol.34 , pp. 893-903
    • Knight, J.L.1    Yesselman, J.D.2    Brooks, C.I.3
  • 66
    • 33644532518 scopus 로고    scopus 로고
    • Can free energy calculations be fast and accurate at the same time? Binding of low-affinity, non-peptide inhibitors to the SH2 domain of the src protein
    • Chipot C, Rozanska X, Dixit SB. Can free energy calculations be fast and accurate at the same time? Binding of low-affinity, non-peptide inhibitors to the SH2 domain of the src protein. J Comput Aided Mol Des 2005, 19:765-770.
    • (2005) J Comput Aided Mol Des , vol.19 , pp. 765-770
    • Chipot, C.1    Rozanska, X.2    Dixit, S.B.3
  • 68
    • 0029757992 scopus 로고    scopus 로고
    • Thermodynamic stability of water molecules in the Bacteriorhodopsin proton channel: a molecular dynamics and free energy perturbation study
    • Roux B, Nina M, Pomès, R, Smith JC. Thermodynamic stability of water molecules in the Bacteriorhodopsin proton channel: a molecular dynamics and free energy perturbation study. Biophys J 1996, 71:670-681.
    • (1996) Biophys J , vol.71 , pp. 670-681
    • Roux, B.1    Nina, M.2    Pomès, R.3    Smith, J.C.4
  • 69
    • 0031058541 scopus 로고    scopus 로고
    • The statistical-thermodynamic basis for computation of binding affinities: a critical review
    • Gilson MK, Given JA, Bush BL, McCammon, JA. The statistical-thermodynamic basis for computation of binding affinities: a critical review. Biophys J 1997, 72:1047-1069.
    • (1997) Biophys J , vol.72 , pp. 1047-1069
    • Gilson, M.K.1    Given, J.A.2    Bush, B.L.3    McCammon, J.A.4
  • 70
    • 0030887944 scopus 로고    scopus 로고
    • Inclusion of loss of translational and rotational freedom in theoretical estimates of free energies of binding. Application to a complex of benzene and mutant T4 lysozyme
    • Hermans J, Wang L. Inclusion of loss of translational and rotational freedom in theoretical estimates of free energies of binding. Application to a complex of benzene and mutant T4 lysozyme. J Am Chem Soc 1997, 119:2707-2714.
    • (1997) J Am Chem Soc , vol.119 , pp. 2707-2714
    • Hermans, J.1    Wang, L.2
  • 71
    • 0035950796 scopus 로고    scopus 로고
    • Can absolute free energies of association be estimated from molecular mechanical simulations? The biotin-streptavidin system revisited
    • Dixit SB, Chipot C. Can absolute free energies of association be estimated from molecular mechanical simulations? The biotin-streptavidin system revisited. J Phys Chem A 2001, 105:9795-9799.
    • (2001) J Phys Chem A , vol.105 , pp. 9795-9799
    • Dixit, S.B.1    Chipot, C.2
  • 72
    • 18744372751 scopus 로고    scopus 로고
    • Calculation of absolute protein-ligand binding free energy from computer simulations
    • Woo HJ, Roux B. Calculation of absolute protein-ligand binding free energy from computer simulations. Proc Natl Acad Sci USA 2005, 102:6825-6830.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 6825-6830
    • Woo, H.J.1    Roux, B.2
  • 73
    • 77955578745 scopus 로고    scopus 로고
    • A note on the standard state's binding free energy
    • General IJ. A note on the standard state's binding free energy. J Chem Theor Comput 2010, 6:2520-2524.
    • (2010) J Chem Theor Comput , vol.6 , pp. 2520-2524
    • General, I.J.1
  • 74
    • 0030059225 scopus 로고    scopus 로고
    • Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force
    • Grubmü
    • Grubmüller H, Heymann B, Tavan P. Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force. Science 1996, 271:997-999.
    • (1996) Science , vol.271 , pp. 997-999
    • Grubmüller, H.1    Heymann, B.2    Tavan, P.3
  • 75
    • 65249154272 scopus 로고    scopus 로고
    • Standard free energy of binding from a one-dimensional potential of mean force
    • Doudou S, Burton NA, Henchman RH. Standard free energy of binding from a one-dimensional potential of mean force. J Chem Theor Comput 2009, 5:909-918.
    • (2009) J Chem Theor Comput , vol.5 , pp. 909-918
    • Doudou, S.1    Burton, N.A.2    Henchman, R.H.3
  • 79
    • 79960007037 scopus 로고    scopus 로고
    • Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
    • Buch I, Giorgino T, De Fabritiis G. Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations. Proc Natl Acad Sci USA 2011, 108:10184-10189.
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 10184-10189
    • Buch, I.1    Giorgino, T.2    De Fabritiis, G.3
  • 81
    • 24344467850 scopus 로고    scopus 로고
    • Transition pathways in complex systems: reaction coordinates, isocommittor surfaces, and transition tubes
    • Weinan E, Ren W, Vanden-Eijnden E. Transition pathways in complex systems: reaction coordinates, isocommittor surfaces, and transition tubes. Chem Phys Lett 2005, 413:242-247.
    • (2005) Chem Phys Lett , vol.413 , pp. 242-247
    • Weinan, E.1    Ren, W.2    Vanden-Eijnden, E.3
  • 82
    • 77950102787 scopus 로고    scopus 로고
    • Exploring multidimensional free energy landscapes using time-dependent biases on collective variables
    • Hénin, J, Forin G, Chipot C, Klein ML. Exploring multidimensional free energy landscapes using time-dependent biases on collective variables. J Chem Theor Comput 2010, 6:35-47.
    • (2010) J Chem Theor Comput , vol.6 , pp. 35-47
    • Hénin, J.1    Forin, G.2    Chipot, C.3    Klein, M.L.4
  • 83
    • 80755182255 scopus 로고    scopus 로고
    • Enhanced sampling of multidimensional free-energy landscapes using adaptive biasing forces
    • Chipot C, Lelièvre, T. Enhanced sampling of multidimensional free-energy landscapes using adaptive biasing forces. SIAM J Appl Math 2011, 71:1673-1695.
    • (2011) SIAM J Appl Math , vol.71 , pp. 1673-1695
    • Chipot, C.1    Lelièvre, T.2
  • 84
    • 0042885340 scopus 로고    scopus 로고
    • Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality
    • Park S, Khalili-Araghi F, Tajkhorshid E, Schulten K. Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality. J Chem Phys 2003, 119:3559-3566.
    • (2003) J Chem Phys , vol.119 , pp. 3559-3566
    • Park, S.1    Khalili-Araghi, F.2    Tajkhorshid, E.3    Schulten, K.4
  • 85
    • 4344660645 scopus 로고    scopus 로고
    • Overcoming free energy barriers using unconstrained molecular dynamics simulations
    • Hénin, J, Chipot C. Overcoming free energy barriers using unconstrained molecular dynamics simulations. J Chem Phys 2004, 121:2904-2914.
    • (2004) J Chem Phys , vol.121 , pp. 2904-2914
    • Hénin, J.1    Chipot, C.2
  • 86
    • 29744459271 scopus 로고    scopus 로고
    • Exploring the free energy landscape of a short peptide using an average force
    • Chipot C, Hénin, J. Exploring the free energy landscape of a short peptide using an average force. J Chem Phys 2005, 123:244906.
    • (2005) J Chem Phys , vol.123 , pp. 244906
    • Chipot, C.1    Hénin, J.2
  • 87
    • 77951140202 scopus 로고    scopus 로고
    • Potential of mean force calculations: a multiple-walker adaptive biasing force approach
    • Minoukadeh K, Chipot C, Lelièvre, T. Potential of mean force calculations: a multiple-walker adaptive biasing force approach. J Chem Theor Comput 2010, 6:1008-1017.
    • (2010) J Chem Theor Comput , vol.6 , pp. 1008-1017
    • Minoukadeh, K.1    Chipot, C.2    Lelièvre, T.3
  • 88
    • 0342929614 scopus 로고
    • Nonphysical sampling distributions in Monte Carlo free energy estimation: umbrella sampling
    • Torrie GM, Valleau JP. Nonphysical sampling distributions in Monte Carlo free energy estimation: umbrella sampling. J Comput Phys 1977, 23:187-199.
    • (1977) J Comput Phys , vol.23 , pp. 187-199
    • Torrie, G.M.1    Valleau, J.P.2
  • 89
    • 0029633155 scopus 로고
    • The calculation of the potential of mean force using computer simulations
    • Roux B. The calculation of the potential of mean force using computer simulations. Comput Phys Comm 1995, 91:275-282.
    • (1995) Comput Phys Comm , vol.91 , pp. 275-282
    • Roux, B.1
  • 90
    • 0028710015 scopus 로고
    • Local elevation: a method for improving the searching properties of molecular dynamics simulation
    • Huber T, Torda AE, van Gunsteren WF. Local elevation: a method for improving the searching properties of molecular dynamics simulation. J Comput Aided Mol Des 1994, 8:695-708.
    • (1994) J Comput Aided Mol Des , vol.8 , pp. 695-708
    • Huber, T.1    Torda, A.E.2    van Gunsteren, W.F.3
  • 91
    • 0000689085 scopus 로고
    • Predicting slow structural transitions in macromolecular systems: conformational flooding
    • Grubmüller H.
    • Grubmüller H. Predicting slow structural transitions in macromolecular systems: conformational flooding. Phys Rev E 1995, 52:2893-2906.
    • (1995) Phys Rev E , vol.52 , pp. 2893-2906
  • 93
    • 0035935802 scopus 로고    scopus 로고
    • Calculating free energies using average force
    • Darve E, Pohorille A. Calculating free energies using average force. J Chem Phys 2001, 115:9169-9183.
    • (2001) J Chem Phys , vol.115 , pp. 9169-9183
    • Darve, E.1    Pohorille, A.2
  • 94
    • 4243661501 scopus 로고
    • Constrained reaction coordinate dynamics for the simulation of rare events
    • Carter E, Ciccotti G, Hynes JT, Kapral R. Constrained reaction coordinate dynamics for the simulation of rare events. Chem Phys Lett 1989, 156:472-477.
    • (1989) Chem Phys Lett , vol.156 , pp. 472-477
    • Carter, E.1    Ciccotti, G.2    Hynes, J.T.3    Kapral, R.4
  • 95
    • 20444499328 scopus 로고    scopus 로고
    • Insights into the recognition and association of transmembrane α-helices. The free energy of α-helix dimerization in glycophorin A
    • Hénin J
    • Hénin J, Pohorille A, Chipot C. Insights into the recognition and association of transmembrane α-helices. The free energy of α-helix dimerization in glycophorin A. J Am Chem Soc 2005, 127:8478-8484.
    • (2005) J Am Chem Soc , vol.127 , pp. 8478-8484
    • Pohorille, A.1    Chipot, C.2
  • 96
    • 0031144465 scopus 로고    scopus 로고
    • Hyperdynamics: accelerated molecular dynamics of infrequent events
    • Voter AF. Hyperdynamics: accelerated molecular dynamics of infrequent events. Phys Rev Lett 1997, 78:3908-3911.
    • (1997) Phys Rev Lett , vol.78 , pp. 3908-3911
    • Voter, A.F.1
  • 97
    • 33745762636 scopus 로고    scopus 로고
    • A temperature accelerated method for sampling free energy and determining reaction pathways in rare events simulations
    • Maragliano L, Vanden-Eijnden E. A temperature accelerated method for sampling free energy and determining reaction pathways in rare events simulations. Chem Phys Lett 2006, 426:168-175.
    • (2006) Chem Phys Lett , vol.426 , pp. 168-175
    • Maragliano, L.1    Vanden-Eijnden, E.2
  • 98
    • 0035498860 scopus 로고    scopus 로고
    • + channel
    • Bernèche S
    • + channel. Nature 2001, 414:73-77.
    • (2001) Nature , vol.414 , pp. 73-77
    • Roux, B.1
  • 99
    • 0347089020 scopus 로고    scopus 로고
    • Energetics of ion conduction through the gramicidin channel
    • Allen TW, Andersen OS, Roux B. Energetics of ion conduction through the gramicidin channel. Proc Natl Acad Sci USA 2004, 101:117-122.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 117-122
    • Allen, T.W.1    Andersen, O.S.2    Roux, B.3
  • 101
    • 78650127789 scopus 로고    scopus 로고
    • Computing ensembles of transitions from stable states: dynamic importance sampling
    • Perilla JR, Beckstein O, Denning EJ, Woolf TB. Computing ensembles of transitions from stable states: dynamic importance sampling. J Comput Chem 2011, 32:196-209.
    • (2011) J Comput Chem , vol.32 , pp. 196-209
    • Perilla, J.R.1    Beckstein, O.2    Denning, E.J.3    Woolf, T.B.4
  • 102
    • 79952354508 scopus 로고    scopus 로고
    • The hidden energetics of ligand binding and activation in a glutamate receptor
    • Lau AY, Roux B. The hidden energetics of ligand binding and activation in a glutamate receptor. Nat Struct Mol Biol 2011, 18:283-287.
    • (2011) Nat Struct Mol Biol , vol.18 , pp. 283-287
    • Lau, A.Y.1    Roux, B.2
  • 103
    • 84882330872 scopus 로고    scopus 로고
    • Efficient determination of protein-protein standard binding free energies from first principles
    • in revision)
    • Gumbart JC, Roux B, Chipot C. Efficient determination of protein-protein standard binding free energies from first principles. J Chem Theor Comput 2013 (in revision).
    • (2013) J Chem Theor Comput
    • Gumbart, J.C.1    Roux, B.2    Chipot, C.3
  • 104
    • 80052315342 scopus 로고    scopus 로고
    • Oligomerization state of photosynthetic core complexes is correlated with the dimerization affinity of a transmembrane helix
    • Hsin J, LaPointe LM, Kazy A, Chipot C, Senes A, Schulten K. Oligomerization state of photosynthetic core complexes is correlated with the dimerization affinity of a transmembrane helix. J Am Chem Soc 2011, 133:14071-14081.
    • (2011) J Am Chem Soc , vol.133 , pp. 14071-14081
    • Hsin, J.1    LaPointe, L.M.2    Kazy, A.3    Chipot, C.4    Senes, A.5    Schulten, K.6
  • 105
    • 84872165531 scopus 로고    scopus 로고
    • Standard binding free energies from computer simulations: what is the best strategy?
    • Gumbart JC, Roux B, Chipot C. Standard binding free energies from computer simulations: what is the best strategy? J Chem Theor Comput 2013, 9:794-802.
    • (2013) J Chem Theor Comput , vol.9 , pp. 794-802
    • Gumbart, J.C.1    Roux, B.2    Chipot, C.3
  • 107
    • 0035957434 scopus 로고    scopus 로고
    • Free energy reconstruction from nonequilibrium single-molecule pulling experiments
    • Hummer G, Szabo A. Free energy reconstruction from nonequilibrium single-molecule pulling experiments. Proc Natl Acad Sci USA 2001, 98:3658-3661.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 3658-3661
    • Hummer, G.1    Szabo, A.2
  • 108
    • 0032023968 scopus 로고    scopus 로고
    • Nonequilibrium measurements of free energy differences for microscopically reversible Markovian systems
    • Crooks GE. Nonequilibrium measurements of free energy differences for microscopically reversible Markovian systems. J Stat Phys 1998, 90:1481-1487.
    • (1998) J Stat Phys , vol.90 , pp. 1481-1487
    • Crooks, G.E.1
  • 109
    • 33645010025 scopus 로고    scopus 로고
    • Optimal estimates of free energies from multistate nonequilibrium work data
    • Maragakis P, Spichty M, Karplus M. Optimal estimates of free energies from multistate nonequilibrium work data. Phys Rev Lett 2006, 96:100602.
    • (2006) Phys Rev Lett , vol.96 , pp. 100602
    • Maragakis, P.1    Spichty, M.2    Karplus, M.3
  • 110
  • 111
    • 38849088221 scopus 로고    scopus 로고
    • Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF
    • Hénin, J, Tajkhorshid E, Schulten K, Chipot C. Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF. Biophys J 2008, 94:832-839.
    • (2008) Biophys J , vol.94 , pp. 832-839
    • Hénin, J.1    Tajkhorshid, E.2    Schulten, K.3    Chipot, C.4
  • 112
    • 39549085136 scopus 로고    scopus 로고
    • Mechanism of selectivity in aquaporins and aquaglyceroporins
    • Hub JS, de Groot BL. Mechanism of selectivity in aquaporins and aquaglyceroporins. Proc Natl Acad Sci USA 2008, 105:1198-1203.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 1198-1203
    • Hub, J.S.1    de Groot, B.L.2
  • 113
    • 77952844866 scopus 로고    scopus 로고
    • Single-molecule pulling simulations can discern active from inactive enzyme inhibitors
    • Colizzi F, Perozzo R, Scapozza L, Recanatini M, Cavalli A. Single-molecule pulling simulations can discern active from inactive enzyme inhibitors. J Am Chem Soc 2010, 132:7361-7371.
    • (2010) J Am Chem Soc , vol.132 , pp. 7361-7371
    • Colizzi, F.1    Perozzo, R.2    Scapozza, L.3    Recanatini, M.4    Cavalli, A.5
  • 114
    • 0031578972 scopus 로고    scopus 로고
    • Parallel tempering algorithm for conformational studies of biological molecules
    • Hansmann UHE. Parallel tempering algorithm for conformational studies of biological molecules. Chem Phys Lett 1997, 281:140-150.
    • (1997) Chem Phys Lett , vol.281 , pp. 140-150
    • Hansmann, U.H.E.1
  • 115
    • 0034294024 scopus 로고    scopus 로고
    • Multidimensional replica-exchange method for free-energy calculations
    • Sugita Y, Kitao A, Okamoto Y. Multidimensional replica-exchange method for free-energy calculations. J Chem Phys 2000, 113:6042-6051.
    • (2000) J Chem Phys , vol.113 , pp. 6042-6051
    • Sugita, Y.1    Kitao, A.2    Okamoto, Y.3
  • 116
    • 0346350789 scopus 로고    scopus 로고
    • The development of replica-exchange-based free-energy methods
    • Woods CJ, Essex JW, King MA. The development of replica-exchange-based free-energy methods. J Phys Chem B 2003, 107:13703-13710.
    • (2003) J Phys Chem B , vol.107 , pp. 13703-13710
    • Woods, C.J.1    Essex, J.W.2    King, M.A.3
  • 117
    • 77956574437 scopus 로고    scopus 로고
    • Free energy perturbation Hamiltonian replica-exchange molecular dynamics (FEP/H-REMD) for absolute ligand binding free energy calculations
    • 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.
    • (2010) J Chem Theory Comput , vol.6 , pp. 2559-2565
    • Jiang, W.1    Roux, B.2
  • 118
    • 58149512801 scopus 로고    scopus 로고
    • Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems
    • Zheng L, Chen M, Yang W. Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems. Proc Natl Acad Sci USA 2008, 105:20227-20232.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 20227-20232
    • Zheng, L.1    Chen, M.2    Yang, W.3
  • 119
    • 77956154559 scopus 로고    scopus 로고
    • Downhill binding energy surface of the barnase-barstar complex
    • Wang L, Siu SWI, Gu W, Helms V. Downhill binding energy surface of the barnase-barstar complex. Biopolymers 2010, 93:977-985.
    • (2010) Biopolymers , vol.93 , pp. 977-985
    • Wang, L.1    Siu, S.W.I.2    Gu, W.3    Helms, V.4
  • 120
    • 84863535732 scopus 로고    scopus 로고
    • Structural determinants of the supramolecular organization of G protein-coupled receptors in bilayers
    • Periole X, Knepp AM, Sakmar TP, Marrink SJ, Huber T. Structural determinants of the supramolecular organization of G protein-coupled receptors in bilayers. J Am Chem Soc 2012, 134:10959-10965.
    • (2012) J Am Chem Soc , vol.134 , pp. 10959-10965
    • Periole, X.1    Knepp, A.M.2    Sakmar, T.P.3    Marrink, S.J.4    Huber, T.5
  • 121
    • 23244438863 scopus 로고    scopus 로고
    • Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations
    • doi:10.1088/1367-2630/7/1/034
    • Hummer G. Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations. New J Phys 2005, 7:34. doi:10.1088/1367-2630/7/1/034
    • (2005) New J Phys , vol.7 , pp. 34
    • Hummer, G.1
  • 122
    • 84873665160 scopus 로고    scopus 로고
    • Calculating position-dependent diffusivity in biased molecular dynamics simulations
    • Comer J, Chipot C, González-Nilo FD. Calculating position-dependent diffusivity in biased molecular dynamics simulations. J Chem Theor Comput 2013, 9:876-882.
    • (2013) J Chem Theor Comput , vol.9 , pp. 876-882
    • Comer, J.1    Chipot, C.2    González-Nilo, F.D.3


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