메뉴 건너뛰기




Volumn 22, Issue 5, 2004, Pages 359-368

Tools for channels: Moving towards molecular calculations of gating and permeation in ion channel biophysics

Author keywords

Importance sampling; Ion channels; Kinetics; Molecular dynamics; Non equilibrium free energy; Overlap sampling; Permeation; Relative free energy

Indexed keywords

COMPUTATIONAL METHODS; ELECTRIC POTENTIAL; FREE ENERGY; FUNCTIONS; IONS; MOLECULAR STRUCTURE; POTASSIUM; SAMPLING; X RAY ANALYSIS;

EID: 1942504108     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2003.12.003     Document Type: Conference Paper
Times cited : (15)

References (78)
  • 1
    • 35649001607 scopus 로고
    • A quantitative description of membrane current and its application to conduction and excitation in nerve
    • Hodgkin A.L., Huxley A.F. A quantitative description of membrane current and its application to conduction and excitation in nerve. J. Physiol. (Lond.). 117:1952;500-544.
    • (1952) J. Physiol. (Lond.) , vol.117 , pp. 500-544
    • Hodgkin, A.L.1    Huxley, A.F.2
  • 3
    • 0034017867 scopus 로고    scopus 로고
    • The voltage sensor in voltage-dependent ion channels
    • Bezanilla F. The voltage sensor in voltage-dependent ion channels. Physiol. Rev. 80:2000;555-592.
    • (2000) Physiol. Rev. , vol.80 , pp. 555-592
    • Bezanilla, F.1
  • 4
    • 0027971204 scopus 로고
    • Voltage gating of ion channels
    • Sigworth F.J. Voltage gating of ion channels. Q. Rev. Biophys. 27:1994;1-40.
    • (1994) Q. Rev. Biophys. , vol.27 , pp. 1-40
    • Sigworth, F.J.1
  • 5
    • 0037198626 scopus 로고    scopus 로고
    • Crystal structure and mechanism of a calcium-gated potassium channel
    • Jiang Y.X., Lee A., Chen J.Y., Cadene M., Chait B.T., MacKinnon R. Crystal structure and mechanism of a calcium-gated potassium channel. Nature. 417:2002;515-522.
    • (2002) Nature , vol.417 , pp. 515-522
    • Jiang, Y.X.1    Lee, A.2    Chen, J.Y.3    Cadene, M.4    Chait, B.T.5    MacKinnon, R.6
  • 8
    • 0038752614 scopus 로고    scopus 로고
    • The principle of gating charge movement in a voltage-dependent K-channel
    • Jiang Y.X., Ruta V., Chen J.Y., Lee A., MacKinnon R. The principle of gating charge movement in a voltage-dependent K-channel. Nature. 423:2003;42-48.
    • (2003) Nature , vol.423 , pp. 42-48
    • Jiang, Y.X.1    Ruta, V.2    Chen, J.Y.3    Lee, A.4    MacKinnon, R.5
  • 10
    • 0037435021 scopus 로고    scopus 로고
    • Functional analysis of an archaebacterial voltage-dependent K-channel
    • Ruta V., Jiang Y.X., Lee A., Chen J.Y., MacKinnon R. Functional analysis of an archaebacterial voltage-dependent K-channel. Nature. 422:2003;180-185.
    • (2003) Nature , vol.422 , pp. 180-185
    • Ruta, V.1    Jiang, Y.X.2    Lee, A.3    Chen, J.Y.4    MacKinnon, R.5
  • 11
    • 0021691918 scopus 로고
    • An analysis of incorrectly folded protein models: Implications for structure predictions
    • Novotny J., Bruccoleri R., Karplus M. An analysis of incorrectly folded protein models: implications for structure predictions. J. Mol. Biol. 177:1984;787-818.
    • (1984) J. Mol. Biol. , vol.177 , pp. 787-818
    • Novotny, J.1    Bruccoleri, R.2    Karplus, M.3
  • 12
    • 0141927102 scopus 로고    scopus 로고
    • Molecular dynamics simulation of dark-adapted rhodopsin in an explicit membrane bilayer: Coupling between local retinal and larger scale conformational change
    • Crozier P.S., Stevens M.J., Forrest L.R., Woolf T.B. Molecular dynamics simulation of dark-adapted rhodopsin in an explicit membrane bilayer: coupling between local retinal and larger scale conformational change. J. Mol. Biol. 333:2003;493-514.
    • (2003) J. Mol. Biol. , vol.333 , pp. 493-514
    • Crozier, P.S.1    Stevens, M.J.2    Forrest, L.R.3    Woolf, T.B.4
  • 13
    • 3042660129 scopus 로고
    • A statistical-method for identifying transition-states in high dimensional problems
    • Pratt L.R. A statistical-method for identifying transition-states in high dimensional problems. J. Chem. Phys. 85:1986;5045-5048.
    • (1986) J. Chem. Phys. , vol.85 , pp. 5045-5048
    • Pratt, L.R.1
  • 14
    • 0011690263 scopus 로고
    • Locating stationary paths in functional-integrals: An optimization method utilizing the stationary phase Monte-Carlo sampling function
    • Beck T.L., Doll J.D., Freeman D.L. Locating stationary paths in functional-integrals: an optimization method utilizing the stationary phase Monte-Carlo sampling function. J. Chem. Phys. 90:1989;3181-3191.
    • (1989) J. Chem. Phys. , vol.90 , pp. 3181-3191
    • Beck, T.L.1    Doll, J.D.2    Freeman, D.L.3
  • 15
    • 0001210312 scopus 로고
    • The construction of double-ended classical trajectories
    • Cho A.E., Doll J.D., Freeman D.L. The construction of double-ended classical trajectories. Chem. Phys. Lett. 229:1994;218-224.
    • (1994) Chem. Phys. Lett. , vol.229 , pp. 218-224
    • Cho, A.E.1    Doll, J.D.2    Freeman, D.L.3
  • 16
    • 36449008311 scopus 로고
    • Shadowing, rare events, and rubber bands - A variational verlet algorithm for molecular-dynamics
    • Gillilan R.E., Wilson K.R. Shadowing, rare events, and rubber bands - a variational verlet algorithm for molecular-dynamics. J. Chem. Phys. 97:1992;1757-1772.
    • (1992) J. Chem. Phys. , vol.97 , pp. 1757-1772
    • Gillilan, R.E.1    Wilson, K.R.2
  • 17
    • 0031256658 scopus 로고    scopus 로고
    • The MaxFlux algorithm for calculating variationally optimized reaction paths for conformational transitions in many body systems at finite temperature
    • Huo S.H., Straub J.E. The MaxFlux algorithm for calculating variationally optimized reaction paths for conformational transitions in many body systems at finite temperature. J. Chem. Phys. 107:1997;5000-5006.
    • (1997) J. Chem. Phys. , vol.107 , pp. 5000-5006
    • Huo, S.H.1    Straub, J.E.2
  • 18
    • 0038459088 scopus 로고
    • Locating transition-states using double-ended classical trajectories
    • Matro A., Freeman D.L., Doll J.D. Locating transition-states using double-ended classical trajectories. J. Chem. Phys. 101:1994;10458-10463.
    • (1994) J. Chem. Phys. , vol.101 , pp. 10458-10463
    • Matro, A.1    Freeman, D.L.2    Doll, J.D.3
  • 19
    • 0001506011 scopus 로고
    • A chain of states method for investigating infrequent event processes occurring in multistate, multi-dimensional systems
    • Sevick E.M., Bell A.T., Theodorou D.N. A chain of states method for investigating infrequent event processes occurring in multistate, multi-dimensional systems. J. Chem. Phys. 98:1993;3196-3212.
    • (1993) J. Chem. Phys. , vol.98 , pp. 3196-3212
    • Sevick, E.M.1    Bell, A.T.2    Theodorou, D.N.3
  • 20
    • 0000191981 scopus 로고
    • Reaction-path study of conformational transitions in flexible systems: Applications to peptides
    • Czerminski R., Elber R. Reaction-path study of conformational transitions in flexible systems: applications to peptides. J. Chem. Phys. 92:1990;5580-5601.
    • (1990) J. Chem. Phys. , vol.92 , pp. 5580-5601
    • Czerminski, R.1    Elber, R.2
  • 21
    • 84987058840 scopus 로고
    • Self-avoiding walk between 2 fixed-points as a tool to calculate reaction paths in large molecular-systems
    • Czerminski R., Elber R. Self-avoiding walk between 2 fixed-points as a tool to calculate reaction paths in large molecular-systems. Int. J. Quantum Chem. Suppl. 24:1990;167-186.
    • (1990) Int. J. Quantum Chem. , vol.24 , pp. 167-186
    • Czerminski, R.1    Elber, R.2
  • 22
    • 0000231955 scopus 로고
    • Conjugate peak refinement: An algorithm for finding reaction paths and accurate transition-states in systems with many degrees of freedom
    • Fischer S., Karplus S.M. Conjugate peak refinement: an algorithm for finding reaction paths and accurate transition-states in systems with many degrees of freedom. Chem. Phys. Lett. 194:1992;252-261.
    • (1992) Chem. Phys. Lett. , vol.194 , pp. 252-261
    • Fischer, S.1    Karplus, S.M.2
  • 23
    • 33748374124 scopus 로고
    • Statistical-mechanis of isomerization dynamics in liquids and transition-state aproximation
    • Chandler D. Statistical-mechanis of isomerization dynamics in liquids and transition-state aproximation. J. Chem. Phys. 68:1978;2959-2970.
    • (1978) J. Chem. Phys. , vol.68 , pp. 2959-2970
    • Chandler, D.1
  • 24
    • 0000729781 scopus 로고    scopus 로고
    • Transition path sampling and the calculation of rate constants
    • Dellago C., Bolhuis P.G., Csajka F.S., Chandler D. Transition path sampling and the calculation of rate constants. J. Chem. Phys. 108:1998;1964-1977.
    • (1998) J. Chem. Phys. , vol.108 , pp. 1964-1977
    • Dellago, C.1    Bolhuis, P.G.2    Csajka, F.S.3    Chandler, D.4
  • 25
    • 0032547683 scopus 로고    scopus 로고
    • Computing probabilities of very rare events for Langevin processes: A new method based on importance sampling
    • Mazonka O., Jarzynski C., Blocki J. Computing probabilities of very rare events for Langevin processes: a new method based on importance sampling. Nucl. Phys. A. 641:1998;335-354.
    • (1998) Nucl. Phys. a , vol.641 , pp. 335-354
    • Mazonka, O.1    Jarzynski, C.2    Blocki, J.3
  • 26
    • 0032546697 scopus 로고    scopus 로고
    • Path corrected functionals of stochastic trajectories: Towards relative free energy and reaction coordinate calculations
    • Woolf T.B. Path corrected functionals of stochastic trajectories: towards relative free energy and reaction coordinate calculations. Chem. Phys. Lett. 289:1998;433-441.
    • (1998) Chem. Phys. Lett. , vol.289 , pp. 433-441
    • Woolf, T.B.1
  • 27
    • 0012021417 scopus 로고    scopus 로고
    • Calculation of classical trajectories with a very large time step: Formalism and numerical examples
    • Olender R., Elber R. Calculation of classical trajectories with a very large time step: formalism and numerical examples. J. Chem. Phys. 105:1996;9299-9315.
    • (1996) J. Chem. Phys. , vol.105 , pp. 9299-9315
    • Olender, R.1    Elber, R.2
  • 28
    • 0000765740 scopus 로고    scopus 로고
    • Stochastic construction of reaction paths: A genetic algorithm-based approach
    • Chaudhury P., Bhattacharyya S.P. Stochastic construction of reaction paths: a genetic algorithm-based approach. Int. J. Quantum Chem. 76:2000;161-168.
    • (2000) Int. J. Quantum Chem. , vol.76 , pp. 161-168
    • Chaudhury, P.1    Bhattacharyya, S.P.2
  • 29
    • 37649032676 scopus 로고    scopus 로고
    • Finding transition paths and rate coefficients through accelerated Langevin dynamics
    • (art. no. 042101).
    • L.Y. Chen, S.C. Ying, T. Ala-Nissila, Finding transition paths and rate coefficients through accelerated Langevin dynamics, Phys. Rev. E 65 (2002) (art. no. 042101).
    • (2002) Phys. Rev. E , vol.65
    • Chen, L.Y.1    Ying, S.C.2    Ala-Nissila, T.3
  • 30
    • 0037439832 scopus 로고    scopus 로고
    • Efficient thermal rate constant calculation for rare event systems
    • Corcelli S.A., Rahman J.A., Tully J.C. Efficient thermal rate constant calculation for rare event systems. J. Chem. Phys. 118:2003;1085-1088.
    • (2003) J. Chem. Phys. , vol.118 , pp. 1085-1088
    • Corcelli, S.A.1    Rahman, J.A.2    Tully, J.C.3
  • 31
    • 0035250027 scopus 로고    scopus 로고
    • Simulation of protein folding by reaction path annealing
    • Eastman P., Gronbech-Jensen N., Doniach S. Simulation of protein folding by reaction path annealing. J. Chem. Phys. 114:2001;3823-3841.
    • (2001) J. Chem. Phys. , vol.114 , pp. 3823-3841
    • Eastman, P.1    Gronbech-Jensen, N.2    Doniach, S.3
  • 32
    • 0036696910 scopus 로고    scopus 로고
    • String method for the study of rare events
    • (art. no. 052301).
    • W.N. E, W.Q. Ren, E. Vanden-Eijnden, String method for the study of rare events, Phys. Rev. B 66 (2002) (art. no. 052301).
    • (2002) Phys. Rev. B , vol.66
    • E, W.N.1    Ren, W.Q.2    Vanden-Eijnden, E.3
  • 33
    • 0037865691 scopus 로고    scopus 로고
    • Coarse molecular dynamics of a peptide fragment: Free energy, kinetics, and long-time dynamics computations
    • Hummer G., Kevrekidis I.G. Coarse molecular dynamics of a peptide fragment: free energy, kinetics, and long-time dynamics computations. J. Chem. Phys. 118:2003;10762-10773.
    • (2003) J. Chem. Phys. , vol.118 , pp. 10762-10773
    • Hummer, G.1    Kevrekidis, I.G.2
  • 34
    • 41349105094 scopus 로고    scopus 로고
    • Targeted free energy perturbation
    • (art. no. 046122, Part 2A).
    • C. Jarzynski, Targeted free energy perturbation, Phys. Rev. E 65 (2002) (art. no. 046122, Part 2A).
    • (2002) Phys. Rev. e , vol.65
    • Jarzynski, C.1
  • 35
    • 0036708474 scopus 로고    scopus 로고
    • Efficient generation of feasible pathways for protein conformational transitions
    • Kim M.K., Jernigan R.L., Chirikjian G.S. Efficient generation of feasible pathways for protein conformational transitions. Biophys. J. 83:2002;1620-1630.
    • (2002) Biophys. J. , vol.83 , pp. 1620-1630
    • Kim, M.K.1    Jernigan, R.L.2    Chirikjian, G.S.3
  • 37
    • 0037425870 scopus 로고    scopus 로고
    • Algorithms and novel applications based on the isokinetic ensemble. I. Biophysical and path integral molecular dynamics
    • Minary P., Martyna G.J., Tuckerman M.E. Algorithms and novel applications based on the isokinetic ensemble. I. Biophysical and path integral molecular dynamics. J. Chem. Phys. 118:2003;2510-2526.
    • (2003) J. Chem. Phys. , vol.118 , pp. 2510-2526
    • Minary, P.1    Martyna, G.J.2    Tuckerman, M.E.3
  • 38
    • 0037080723 scopus 로고    scopus 로고
    • Predicting unimolecular chemical reactions: Chemical flooding
    • Muller E.M., de Meijere A., Grubmuller H. Predicting unimolecular chemical reactions: chemical flooding. J. Chem. Phys. 116:2002;897-905.
    • (2002) J. Chem. Phys. , vol.116 , pp. 897-905
    • Muller, E.M.1    De Meijere, A.2    Grubmuller, H.3
  • 39
    • 39249083909 scopus 로고    scopus 로고
    • Action-derived molecular dynamics in the study of rare events
    • (art. no. 108302).
    • D. Passerone, M. Parrinello, Action-derived molecular dynamics in the study of rare events, Phys. Rev. Lett. 87 (2001) (art. no. 108302).
    • (2001) Phys. Rev. Lett. , vol.87
    • Passerone, D.1    Parrinello, M.2
  • 40
    • 0037326677 scopus 로고    scopus 로고
    • A concerted variational strategy for investigating rare events
    • Passerone D., Ceccarelli M., Parrinello M. A concerted variational strategy for investigating rare events. J. Chem. Phys. 118:2003;2025-2032.
    • (2003) J. Chem. Phys. , vol.118 , pp. 2025-2032
    • Passerone, D.1    Ceccarelli, M.2    Parrinello, M.3
  • 41
    • 0038003008 scopus 로고    scopus 로고
    • Biasing a transition state search to locate multiple reaction pathways
    • Peters B., Liang W.Z., Bell A.T. Biasing a transition state search to locate multiple reaction pathways. J. Chem. Phys. 118:2003;9533-9541.
    • (2003) J. Chem. Phys. , vol.118 , pp. 9533-9541
    • Peters, B.1    Liang, W.Z.2    Bell, A.T.3
  • 42
    • 0038515443 scopus 로고    scopus 로고
    • A novel path sampling method for the calculation of rate constant
    • van Erp T.S., Moroni D., Bolhuis P.G. A novel path sampling method for the calculation of rate constant. J. Chem. Phys. 118:2003;7762-7774.
    • (2003) J. Chem. Phys. , vol.118 , pp. 7762-7774
    • Van Erp, T.S.1    Moroni, D.2    Bolhuis, P.G.3
  • 43
    • 0037145606 scopus 로고    scopus 로고
    • Discrete path sampling
    • Wales D.J. Discrete path sampling. Mol. Phys. 100:2002;3285-3305.
    • (2002) Mol. Phys. , vol.100 , pp. 3285-3305
    • Wales, D.J.1
  • 44
    • 0036424048 scopus 로고    scopus 로고
    • Transition path sampling: Throwing ropes over rough mountain passes, in the dark
    • Bolhuis P.G., Chandler D., Dellago C., Geissler P.L. Transition path sampling: throwing ropes over rough mountain passes, in the dark. Annu. Rev. Phys. Chem. 53:2002;291-318.
    • (2002) Annu. Rev. Phys. Chem. , vol.53 , pp. 291-318
    • Bolhuis, P.G.1    Chandler, D.2    Dellago, C.3    Geissler, P.L.4
  • 45
    • 0034321137 scopus 로고    scopus 로고
    • Transition path sampling of cavitation between molecular scale solvophobic surfaces
    • Bolhuis P.G., Chandler D. Transition path sampling of cavitation between molecular scale solvophobic surfaces. J. Chem. Phys. 113:2000;8154-8160.
    • (2000) J. Chem. Phys. , vol.113 , pp. 8154-8160
    • Bolhuis, P.G.1    Chandler, D.2
  • 46
    • 2742515916 scopus 로고    scopus 로고
    • Sampling ensembles of deterministic transition pathways
    • Bolhuis P.G., Dellago C., Chandler D. Sampling ensembles of deterministic transition pathways. Faraday Discuss. 110:1998;421-436.
    • (1998) Faraday Discuss. , vol.110 , pp. 421-436
    • Bolhuis, P.G.1    Dellago, C.2    Chandler, D.3
  • 47
    • 0035419723 scopus 로고    scopus 로고
    • Efficient transition path sampling for non-equilibrium stochastic dynamics
    • (art. no. 026109).
    • G.E. Crooks, D. Chandler, Efficient transition path sampling for non-equilibrium stochastic dynamics, Phys. Rev. E 64 (2001) (art. no. 026109).
    • (2001) Phys. Rev. E , vol.64
    • Crooks, G.E.1    Chandler, D.2
  • 49
    • 4444242987 scopus 로고    scopus 로고
    • On the calculation of reaction rate constants in the transition path ensemble
    • Dellago C., Bolhuis P.G., Chandler D. On the calculation of reaction rate constants in the transition path ensemble. J. Chem. Phys. 110:1999;6617-6625.
    • (1999) J. Chem. Phys. , vol.110 , pp. 6617-6625
    • Dellago, C.1    Bolhuis, P.G.2    Chandler, D.3
  • 50
    • 0000801009 scopus 로고    scopus 로고
    • Efficient transition path sampling: Application to Lennard-Jones cluster rearrangements
    • Dellago C., Bolhuis P.G., Chandler D. Efficient transition path sampling: application to Lennard-Jones cluster rearrangements. J. Chem. Phys. 108:1998;9236-9245.
    • (1998) J. Chem. Phys. , vol.108 , pp. 9236-9245
    • Dellago, C.1    Bolhuis, P.G.2    Chandler, D.3
  • 51
    • 0034507196 scopus 로고    scopus 로고
    • Importance sampling and theory of non-equilibrium solvation dynamics in water
    • Geissler P.L., Chandler D. Importance sampling and theory of non-equilibrium solvation dynamics in water. J. Chem. Phys. 113:2000;9759-9765.
    • (2000) J. Chem. Phys. , vol.113 , pp. 9759-9765
    • Geissler, P.L.1    Chandler, D.2
  • 52
    • 0000778360 scopus 로고    scopus 로고
    • Dynamic reaction paths and rates through importance-sampled stochastic dynamics
    • Zuckerman D.M., Woolf T.B. Dynamic reaction paths and rates through importance-sampled stochastic dynamics. J. Chem. Phys. 111:1999;9475-9484.
    • (1999) J. Chem. Phys. , vol.111 , pp. 9475-9484
    • Zuckerman, D.M.1    Woolf, T.B.2
  • 53
    • 20444367704 scopus 로고    scopus 로고
    • Efficient dynamic importance sampling of rare events in one dimension
    • (art. no. 016702 Part 2).
    • D.M. Zuckerman, T.B. Woolf, Efficient dynamic importance sampling of rare events in one dimension, Phys. Rev E 63 (2001) (art. no. 016702 Part 2).
    • (2001) Phys. Rev E , vol.63
    • Zuckerman, D.M.1    Woolf, T.B.2
  • 54
    • 0037039980 scopus 로고    scopus 로고
    • Transition events in butane simulations: Similarities across models
    • Zuckerman D.M., Woolf T.B. Transition events in butane simulations: similarities across models. J. Chem. Phys. 116:2002;2586-2591.
    • (2002) J. Chem. Phys. , vol.116 , pp. 2586-2591
    • Zuckerman, D.M.1    Woolf, T.B.2
  • 56
    • 0038298804 scopus 로고    scopus 로고
    • Modeling permeation energetics in the KcsA potassium channel
    • Garafoli S., Jordan P.C. Modeling permeation energetics in the KcsA potassium channel. Biophys. J. 84:2003;2814-2830.
    • (2003) Biophys. J. , vol.84 , pp. 2814-2830
    • Garafoli, S.1    Jordan, P.C.2
  • 57
    • 0033516590 scopus 로고    scopus 로고
    • The cavity and pore helices the KcsA K-channel: Electrostatic stabilization of monovalent cations
    • Roux B., MacKinnon R. The cavity and pore helices the KcsA K-channel: electrostatic stabilization of monovalent cations. Science. 285:1999;100-102.
    • (1999) Science , vol.285 , pp. 100-102
    • Roux, B.1    MacKinnon, R.2
  • 58
    • 4243819810 scopus 로고
    • New Monte Carlo technique for studying phase transitions
    • Ferrenberg A.M., Swendsen R.H. New Monte Carlo technique for studying phase transitions. Phys. Rev. Lett. 61:1988;2635-2638.
    • (1988) Phys. Rev. Lett. , vol.61 , pp. 2635-2638
    • Ferrenberg, A.M.1    Swendsen, R.H.2
  • 59
    • 5244304444 scopus 로고
    • Efficient estimation of free-energy differences from Monte Carlo data
    • Bennett C.H. Efficient estimation of free-energy differences from Monte Carlo data. J. Comput. Phys. 22:1976;245-268.
    • (1976) J. Comput. Phys. , vol.22 , pp. 245-268
    • Bennett, C.H.1
  • 60
    • 0038001529 scopus 로고    scopus 로고
    • Staging is more important than perturbation method for computation of enthalpy and entropy changes in complex systems
    • Lu N., Kofke D.A., Woolf T.B. Staging is more important than perturbation method for computation of enthalpy and entropy changes in complex systems. J. Phys. Chem. B. 107:2003;5598-5611.
    • (2003) J. Phys. Chem. B , vol.107 , pp. 5598-5611
    • Lu, N.1    Kofke, D.A.2    Woolf, T.B.3
  • 61
    • 4243754128 scopus 로고    scopus 로고
    • Non-equilibrium equality for free energy differences
    • Jarzynski C. Non-equilibrium equality for free energy differences. Phys. Rev. Lett. 78:1997;2690-2693.
    • (1997) Phys. Rev. Lett. , vol.78 , pp. 2690-2693
    • Jarzynski, C.1
  • 62
    • 4244116139 scopus 로고    scopus 로고
    • Equilibrium free-energy differences from non-equilibrium measurements: A master-equation approach
    • C. Jarzynski, Equilibrium free-energy differences from non-equilibrium measurements: a master-equation approach, Phys. Rev. E 56 (1997) Part A, pp. 5018-5035.
    • (1997) Phys. Rev. E , vol.56 , Issue.PART A , pp. 5018-5035
    • Jarzynski, C.1
  • 63
    • 0035826435 scopus 로고    scopus 로고
    • A "fast growth" method of computing free energy difference
    • Hendrix D.A., Jarzynski C. A "fast growth" method of computing free energy difference. J. Chem. Phys. 114:2001;5974-5981.
    • (2001) J. Chem. Phys. , vol.114 , pp. 5974-5981
    • Hendrix, D.A.1    Jarzynski, C.2
  • 64
    • 0037122460 scopus 로고    scopus 로고
    • Overcoming finite-sampling errors in fast-switching free-energy estimates: Extrapolative analysis of a molecular system
    • Zuckerman D.M., Woolf T.B. Overcoming finite-sampling errors in fast-switching free-energy estimates: extrapolative analysis of a molecular system. Chem. Phys. Lett. 351:2002;445-453.
    • (2002) Chem. Phys. Lett. , vol.351 , pp. 445-453
    • Zuckerman, D.M.1    Woolf, T.B.2
  • 65
    • 18744379822 scopus 로고    scopus 로고
    • Theory of a systematic computational error in free energy differences
    • (art. no. 180602).
    • D.M. Zuckerman, T.B.Woolf, Theory of a systematic computational error in free energy differences, Phys. Rev. Lett. 89 (2002) (art. no. 180602).
    • (2002) Phys. Rev. Lett. , vol.89
    • Zuckerman, D.M.1    Woolf, T.B.2
  • 66
    • 0034333207 scopus 로고    scopus 로고
    • Dipole lattice membrane model for protein calculations
    • Grossfield A., Sachs J., Woolf T.B. Dipole lattice membrane model for protein calculations. Proteins. 41:2000;211-223.
    • (2000) Proteins , vol.41 , pp. 211-223
    • Grossfield, A.1    Sachs, J.2    Woolf, T.B.3
  • 67
    • 36849122972 scopus 로고
    • High-temperature equation of state by a perturbation method
    • Zwanzig R.W. High-temperature equation of state by a perturbation method. J. Chem. Phys. 22:1954;1420-1426.
    • (1954) J. Chem. Phys. , vol.22 , pp. 1420-1426
    • Zwanzig, R.W.1
  • 68
    • 0001556068 scopus 로고    scopus 로고
    • Optimal intermediates in staged free energy calculations
    • Lu N., Kofke D.A. Optimal intermediates in staged free energy calculations. J. Chem. Phys. 111:1999;4414-4423.
    • (1999) J. Chem. Phys. , vol.111 , pp. 4414-4423
    • Lu, N.1    Kofke, D.A.2
  • 69
    • 0035334524 scopus 로고    scopus 로고
    • Accuracy of free-energy perturbation calculations in molecular simulation. I. Modeling
    • Lu N., Kofke D.A. Accuracy of free-energy perturbation calculations in molecular simulation. I. Modeling. J. Chem. Phys. 114:2001;7303-7311.
    • (2001) J. Chem. Phys. , vol.114 , pp. 7303-7311
    • Lu, N.1    Kofke, D.A.2
  • 70
    • 0037440856 scopus 로고    scopus 로고
    • Appropriate methods to combine forward and reverse free energy perturbation averages
    • Lu N., Singh J.K., Kofke D.A. Appropriate methods to combine forward and reverse free energy perturbation averages. J. Chem. Phys. 118:2002;2977-2984.
    • (2002) J. Chem. Phys. , vol.118 , pp. 2977-2984
    • Lu, N.1    Singh, J.K.2    Kofke, D.A.3
  • 71
    • 0345763766 scopus 로고    scopus 로고
    • Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods
    • Lu N., Kofke D.A., Woolf T.B. Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods. J. Comput. Chem. 25:2004;28-39.
    • (2004) J. Comput. Chem. , vol.25 , pp. 28-39
    • Lu, N.1    Kofke, D.A.2    Woolf, T.B.3
  • 72
    • 0001489180 scopus 로고
    • Systematic-errors in free-energy perturbation calculations due to a finite-sample of configuration space sample-size hysteresis
    • Wood R.H., Muhlbauer W.C.F., Thompson P.T. Systematic-errors in free-energy perturbation calculations due to a finite-sample of configuration space sample-size hysteresis. J. Phys. Chem. 95:1991;6670-6675.
    • (1991) J. Phys. Chem. , vol.95 , pp. 6670-6675
    • Wood, R.H.1    Muhlbauer, W.C.F.2    Thompson, P.T.3
  • 73
    • 85085783768 scopus 로고    scopus 로고
    • Systematic finite-sampling inaccuracy in free energy differences and other non-linear quantities
    • in press.
    • D.M. Zuckerman, T.B. Woolf, Systematic finite-sampling inaccuracy in free energy differences and other non-linear quantities, J. Stat. Phys. in press.
    • J. Stat. Phys.
    • Zuckerman, D.M.1    Woolf, T.B.2
  • 74
    • 0038675609 scopus 로고    scopus 로고
    • Effective energy function for proteins in lipid membranes
    • Lazaridis T. Effective energy function for proteins in lipid membranes. Proteins. 52:2003;176-192.
    • (2003) Proteins , vol.52 , pp. 176-192
    • Lazaridis, T.1
  • 75
    • 0037194983 scopus 로고    scopus 로고
    • Introducing an implicit membrane in generalized Born/solvent accessibility continuum solvent models
    • Spassov V.Z., Yan L., Szalma S. Introducing an implicit membrane in generalized Born/solvent accessibility continuum solvent models. J. Phys. Chem. B. 106:2002;8726-8738.
    • (2002) J. Phys. Chem. B. , vol.106 , pp. 8726-8738
    • Spassov, V.Z.1    Yan, L.2    Szalma, S.3
  • 76
    • 0035828343 scopus 로고    scopus 로고
    • Brownian dynamics simulations of ion channels: A general treatment of electrostatic reaction fields for molecular pores of arbitrary geometry
    • Im W., Roux B. Brownian dynamics simulations of ion channels: a general treatment of electrostatic reaction fields for molecular pores of arbitrary geometry. J. Chem. Phys. 115:2001;4850-4861.
    • (2001) J. Chem. Phys. , vol.115 , pp. 4850-4861
    • Im, W.1    Roux, B.2
  • 77
    • 36549097253 scopus 로고
    • The lag between the Hamiltonian and the system configuration in free-energy perturbation calculations
    • Pearlman D.A., Kollman P.A. The lag between the Hamiltonian and the system configuration in free-energy perturbation calculations. J. Chem. Phys. 91:1989;7831-7839.
    • (1989) J. Chem. Phys. , vol.91 , pp. 7831-7839
    • Pearlman, D.A.1    Kollman, P.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.