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Volumn 7, Issue 2, 1997, Pages 181-189

Novel methods of sampling phase space in the simulation of biological systems

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; CHEMICAL STRUCTURE; COMPARATIVE STUDY; CONFORMATION; ELECTRICITY; MOLECULAR BIOLOGY; MOLECULAR DYNAMICS; PRIORITY JOURNAL; REVIEW; SAMPLING; SIMULATION; THERMODYNAMICS;

EID: 0030904524     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(97)80023-1     Document Type: Article
Times cited : (192)

References (76)
  • 1
    • 0000421976 scopus 로고
    • Ergodic behavior in supercooled liquids and glasses
    • Thirumalai D, Mountain RD, Kirkpatrick TR: Ergodic behavior in supercooled liquids and glasses. Phys Rev A 1989, 39:3563-3574.
    • (1989) Phys Rev A , vol.39 , pp. 3563-3574
    • Thirumalai, D.1    Mountain, R.D.2    Kirkpatrick, T.R.3
  • 2
    • 0027972206 scopus 로고
    • Dynamics in rugged energy landscapes with applications to the S-peptide and ribonuclease A
    • Straub JE, Rashkin A, Thirumalai D: Dynamics in rugged energy landscapes with applications to the S-peptide and ribonuclease A. J Am Chem Soc 1994, 116:2049-2063.
    • (1994) J Am Chem Soc , vol.116 , pp. 2049-2063
    • Straub, J.E.1    Rashkin, A.2    Thirumalai, D.3
  • 3
    • 0000441039 scopus 로고
    • Conformational substates and uncertainty in macromolecular free energy calculations
    • Hodel A, Simonsen T, Fox RO, Brünger AT: Conformational substates and uncertainty in macromolecular free energy calculations. J Phys Chem 1993, 97:3409-3417.
    • (1993) J Phys Chem , vol.97 , pp. 3409-3417
    • Hodel, A.1    Simonsen, T.2    Fox, R.O.3    Brünger, A.T.4
  • 6
    • 26044480933 scopus 로고
    • Mass tensor molecular dynamics
    • Bennett CH: Mass tensor molecular dynamics. J Comp Phys 1975, 19:267-279.
    • (1975) J Comp Phys , vol.19 , pp. 267-279
    • Bennett, C.H.1
  • 7
    • 0002667922 scopus 로고
    • Molecular dynamics and Monte Carlo simulations of rare events
    • Edited by Brackbill JU, Cohen BI. New York: Academic Press
    • Berne BJ: Molecular dynamics and Monte Carlo simulations of rare events. In Multiple Time Scales. Edited by Brackbill JU, Cohen BI. New York: Academic Press; 1985:419-436.
    • (1985) Multiple Time Scales , pp. 419-436
    • Berne, B.J.1
  • 8
    • 33646650705 scopus 로고
    • Reversible multiple time scale molecular dynamics
    • Tuckerman ME, Martyna GJ, Berne BJ: Reversible multiple time scale molecular dynamics. J Chem Phys 1992, 97:1990-2001.
    • (1992) J Chem Phys , vol.97 , pp. 1990-2001
    • Tuckerman, M.E.1    Martyna, G.J.2    Berne, B.J.3
  • 9
    • 0001388416 scopus 로고    scopus 로고
    • Molecular dynamics with multiple timescales: The selection of efficient reference system propagators
    • Stuart SJ, Zhou R, Berne BJ: Molecular dynamics with multiple timescales: The selection of efficient reference system propagators. J Chem Phys 1996, 105:1426-1436. Various strategies for factorizing the propagator in r-RESPA are discussed. This paper shows which strategies to avoid and also how to subdivide the Fourier space contribution to the force in Ewald simulations into fast and slow components and how to incorporate this subdivision into an efficient implementation of r-RESPA.
    • (1996) J Chem Phys , vol.105 , pp. 1426-1436
    • Stuart, S.J.1    Zhou, R.2    Berne, B.J.3
  • 10
    • 0000504254 scopus 로고
    • A multiple time scale molecular dynamics algorithm for macromolecules
    • Humphreys D, Friesner RA, Berne BJ: A multiple time scale molecular dynamics algorithm for macromolecules. J Phys Chem 1994, 98:6885-6892.
    • (1994) J Phys Chem , vol.98 , pp. 6885-6892
    • Humphreys, D.1    Friesner, R.A.2    Berne, B.J.3
  • 11
    • 0342744007 scopus 로고
    • Simulated annealing of a protein in a continuum solvent by multiple-time-step molecular dynamics
    • Humphreys D, Friesner RA, Berne BJ: Simulated annealing of a protein in a continuum solvent by multiple-time-step molecular dynamics. J Phys Chem 1995, 99:10674-10685. Building on work in [10], r-RESPA is applied to proteins using the generalized Born solvation model.
    • (1995) J Phys Chem , vol.99 , pp. 10674-10685
    • Humphreys, D.1    Friesner, R.A.2    Berne, B.J.3
  • 12
    • 0009077367 scopus 로고
    • A new molecular dynamics method combining the reference system propagator algorithm with a fast multipole method for simulating proteins and other complex systems
    • Zhou R, Berne BJ: A new molecular dynamics method combining the reference system propagator algorithm with a fast multipole method for simulating proteins and other complex systems. J Chem Phys 1995, 103:9444-9458. This paper combines a new top-down FMM with r-RESPA for simulating proteins. The combination of these two powerful methodologies leads to better than an order of magnitude speed-up for large proteins such as the photosynthetic reaction center.
    • (1995) J Chem Phys , vol.103 , pp. 9444-9458
    • Zhou, R.1    Berne, B.J.2
  • 13
    • 0000240098 scopus 로고
    • Dynamics of molecules with internal degrees of freedom by multiple time-step methods
    • Watanabe M, Karplus M: Dynamics of molecules with internal degrees of freedom by multiple time-step methods. J Chem Phys 1993, 99:8063-8074.
    • (1993) J Chem Phys , vol.99 , pp. 8063-8074
    • Watanabe, M.1    Karplus, M.2
  • 14
    • 0013603851 scopus 로고    scopus 로고
    • Taming the Ewald sum in molecular dynamics simulations of solvated proteins via a multiple time step algorithm
    • Procacci P, Marchi M: Taming the Ewald sum in molecular dynamics simulations of solvated proteins via a multiple time step algorithm. J Chem Phys 1996, 104:3003-3012. In this paper, standard Ewald is combined with r-RESPA. The whole of the Fourier space contribution to the force is included in an outer loop of r-RESPA. Because this sum contains a rapidly varying short time contribution, this is not the best strategy for making the r-RESPA break-up. Despite this, this paper reports a significant speed-up over non-r-RESPA implementations.
    • (1996) J Chem Phys , vol.104 , pp. 3003-3012
    • Procacci, P.1    Marchi, M.2
  • 16
    • 0001257361 scopus 로고
    • On the evaluation of electrostatic interactions in molecular modeling
    • Greengard L, Rokhlin V: On the evaluation of electrostatic interactions in molecular modeling. Phys Scr 1989, 29:139-144.
    • (1989) Phys Scr , vol.29 , pp. 139-144
    • Greengard, L.1    Rokhlin, V.2
  • 17
    • 5544323152 scopus 로고
    • Accelerated molecular dynamics simulation with the parallel fast multipole algorithm
    • Board JA, Causey JW, Leathrum JF, Windemuth A, Schulten K: Accelerated molecular dynamics simulation with the parallel fast multipole algorithm. Chem Phys Lett 1992, 198:89-94.
    • (1992) Chem Phys Lett , vol.198 , pp. 89-94
    • Board, J.A.1    Causey, J.W.2    Leathrum, J.F.3    Windemuth, A.4    Schulten, K.5
  • 18
    • 84986518948 scopus 로고
    • Performance of Fast Multipole Methods for calculating electrostatic interactions in biomacromolecular simulations
    • Shimada J, Kaneko H, Takada T: Performance of Fast Multipole Methods for calculating electrostatic interactions in biomacromolecular simulations. J Comp Chem 1994, 15:28-43.
    • (1994) J Comp Chem , vol.15 , pp. 28-43
    • Shimada, J.1    Kaneko, H.2    Takada, T.3
  • 19
    • 36449006535 scopus 로고
    • Derivation and efficient implementation of the fast multipole method
    • White CA, Head-Gordon M: Derivation and efficient implementation of the fast multipole method. J Chem Phys 1994, 101:6593-6605.
    • (1994) J Chem Phys , vol.101 , pp. 6593-6605
    • White, C.A.1    Head-Gordon, M.2
  • 20
    • 5244247401 scopus 로고
    • Atomic level simulations on a million particles: The cell multipole method for Coulomb and London nonbonded interactions
    • Ding H-Q, Karasawa N, Goddard WA III: Atomic level simulations on a million particles: the cell multipole method for Coulomb and London nonbonded interactions. J Chem Phys 1992, 97:4309-4315.
    • (1992) J Chem Phys , vol.97 , pp. 4309-4315
    • Ding, H.-Q.1    Karasawa, N.2    Goddard W.A. III3
  • 21
    • 0000115003 scopus 로고
    • A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations
    • Lee FS, Warshel A: A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations. J Chem Phys 1992, 97:3100-3107.
    • (1992) J Chem Phys , vol.97 , pp. 3100-3107
    • Lee, F.S.1    Warshel, A.2
  • 22
    • 0000012952 scopus 로고
    • On the treatment of electrostatic interactions in biomolecular simulation
    • Stote RH, States DJ, Karplus M: On the treatment of electrostatic interactions in biomolecular simulation. J Chem Phys 1991, 88:2419-2433.
    • (1991) J Chem Phys , vol.88 , pp. 2419-2433
    • Stote, R.H.1    States, D.J.2    Karplus, M.3
  • 23
    • 0342926714 scopus 로고
    • Molecular dynamics simulations of proteins in water without the truncation of long-range Coulomb interactions
    • Saito M: Molecular dynamics simulations of proteins in water without the truncation of long-range Coulomb interactions. Mol Simulat 1992, 8:321-333.
    • (1992) Mol Simulat , vol.8 , pp. 321-333
    • Saito, M.1
  • 24
    • 0013605528 scopus 로고
    • Efficient calculations of Coulombic interactions in biomolecular simulations with periodic boundary conditions
    • Shimada J, Kaneko H, Takada T: Efficient calculations of Coulombic interactions in biomolecular simulations with periodic boundary conditions. J Comp Chem 1993, 14:867-878.
    • (1993) J Comp Chem , vol.14 , pp. 867-878
    • Shimada, J.1    Kaneko, H.2    Takada, T.3
  • 25
    • 0028063256 scopus 로고
    • Protein simulations using techniques suitable for very large systems: The Cell Multipole Method for nonbonded interactions and the Newton-Euler Inverse Mass Operator Method for internal coordinate dynamics
    • Mathiowetz AM, Jain A, Karasawa N, Goddard WA III: Protein simulations using techniques suitable for very large systems: the Cell Multipole Method for nonbonded interactions and the Newton-Euler Inverse Mass Operator Method for internal coordinate dynamics. Proteins 1994, 20:227-247.
    • (1994) Proteins , vol.20 , pp. 227-247
    • Mathiowetz, A.M.1    Jain, A.2    Karasawa, N.3    Goddard W.A. III4
  • 26
    • 34249919671 scopus 로고
    • Implementing the Fast Multipole Method in three dimensions
    • Lee MA, Schmidt KE: Implementing the Fast Multipole Method in three dimensions. J Stat Phys 1991, 63:1223-1235.
    • (1991) J Stat Phys , vol.63 , pp. 1223-1235
    • Lee, M.A.1    Schmidt, K.E.2
  • 27
    • 33846823909 scopus 로고
    • Particle Mesh Ewald: An N log(N) method for Ewald sums in large systems
    • Darden TA, York DM, Pedersen LG: Particle Mesh Ewald: an N log(N) method for Ewald sums in large systems. J Chem Phys 1993, 98:10089-10092.
    • (1993) J Chem Phys , vol.98 , pp. 10089-10092
    • Darden, T.A.1    York, D.M.2    Pedersen, L.G.3
  • 28
    • 0000577932 scopus 로고
    • Accuracy and efficiency of the Particle Mesh Ewald method
    • Petersen HG: Accuracy and efficiency of the Particle Mesh Ewald method. J Chem Phys 1995, 103:3668-3679.
    • (1995) J Chem Phys , vol.103 , pp. 3668-3679
    • Petersen, H.G.1
  • 30
    • 33751158545 scopus 로고
    • An anisotropic polarizable water model: Incorporation of all-atom polarizabilities into molecular mechanics force fields
    • Bernardo DN, Ding Y, Krogh-Jespersen K, Levy RM: An anisotropic polarizable water model: incorporation of all-atom polarizabilities into molecular mechanics force fields. J Phys Chem 1994, 98:4180-4187.
    • (1994) J Phys Chem , vol.98 , pp. 4180-4187
    • Bernardo, D.N.1    Ding, Y.2    Krogh-Jespersen, K.3    Levy, R.M.4
  • 31
    • 0030197443 scopus 로고    scopus 로고
    • Effects of polarizability on the hydration of the chloride ion
    • Stuart SJ, Berne BJ: Effects of polarizability on the hydration of the chloride ion. J Phys Chem 1996, 100:11934-11943. This paper shows how to incorporate ionic polarizability into a simulation of ionic solubility in polarizable water using the fluctuating charge model and a Drude oscillator polarizability model for the ion. r-RESPA is used to deal with the fast vibrations of the Drude oscillator.
    • (1996) J Phys Chem , vol.100 , pp. 11934-11943
    • Stuart, S.J.1    Berne, B.J.2
  • 32
    • 0001101489 scopus 로고
    • Theory and simulation of polar and non-polar polarizable fluids
    • Cao J, Berne BJ: Theory and simulation of polar and non-polar polarizable fluids. J Chem Phys 1993, 99:6998-7011.
    • (1993) J Chem Phys , vol.99 , pp. 6998-7011
    • Cao, J.1    Berne, B.J.2
  • 33
    • 36448999850 scopus 로고
    • Dynamical fluctuating charge force fields: Application to liquid water
    • Rick SW, Stuart S, Berne BJ: Dynamical fluctuating charge force fields: application to liquid water. J Chem Phys 1994, 101:6141-6161.
    • (1994) J Chem Phys , vol.101 , pp. 6141-6161
    • Rick, S.W.1    Stuart, S.2    Berne, B.J.3
  • 34
    • 0001458825 scopus 로고
    • The aqueous solvation of water: A comparison of molecular and continuum methods
    • Rick SW, Berne BJ: The aqueous solvation of water: a comparison of molecular and continuum methods. J Am Chem Soc 1994, 116:3949-3954.
    • (1994) J Am Chem Soc , vol.116 , pp. 3949-3954
    • Rick, S.W.1    Berne, B.J.2
  • 35
    • 58149211457 scopus 로고
    • Fluctuating charge force fields for aqueous solutions
    • Rick S, Stuart S, Bader JS, Berne BJ: Fluctuating charge force fields for aqueous solutions. J Mol Liq 1995, 65/66:31-40.
    • (1995) J Mol Liq , vol.65-66 , pp. 31-40
    • Rick, S.1    Stuart, S.2    Bader, J.S.3    Berne, B.J.4
  • 36
    • 0000610417 scopus 로고    scopus 로고
    • Dynamical fluctuating charge force fields: The aqueous solvation of amides
    • Rick S, Berne BJ: Dynamical fluctuating charge force fields: the aqueous solvation of amides. J Am Chem Soc 1996, 118:672-679.
    • (1996) J Am Chem Soc , vol.118 , pp. 672-679
    • Rick, S.1    Berne, B.J.2
  • 37
    • 0019014073 scopus 로고
    • Simulation methods for protein structure fluctuations
    • Northup SH, McCammon JA: Simulation methods for protein structure fluctuations. Biopolymers 1980, 19:1001-1016.
    • (1980) Biopolymers , vol.19 , pp. 1001-1016
    • Northup, S.H.1    McCammon, J.A.2
  • 38
    • 0030572603 scopus 로고    scopus 로고
    • Molecular dynamics, Langevin and hybrid Monte Carlo simulations in a mutticanonical ensemble
    • Hannsmann UHE, Okamoto Y, Eisenmenger F: Molecular dynamics, Langevin and hybrid Monte Carlo simulations in a mutticanonical ensemble. Chem Phys Lett 1996, 259:321-330. The paper presents a number of simulation methods based on sampling the multicanonical probability distribution using a variety of algorithms. There is no critical discussion of the relative efficiency of the various algorithms.
    • (1996) Chem Phys Lett , vol.259 , pp. 321-330
    • Hannsmann, U.1    Okamoto, Y.2    Eisenmenger, F.3
  • 39
    • 0001439826 scopus 로고
    • Structure of binary polymer blends: Multiple time step hybrid Monte Carlo simulations and self-consistent integral equation theory
    • Gromov DG, De Pablo JJ: Structure of binary polymer blends: multiple time step hybrid Monte Carlo simulations and self-consistent integral equation theory. J Chem Phys 1995, 103:8247-8256. HMC was first invented in [5]. The need for such a method has an interesting history. Parrinello and Rahman first used MD to simulate quantum degrees of freedom. Calloway and Rahman then showed how MD can be used for lattice-gauge simulations. Hall and Berne pointed out that MD could not often be used by itself to simulate path integrals because the dynamics would often be in the KAM regime where they would not be ergodic. Berne and Hall suggested that one should then punctuate the MD evolution by sampling the momenta from the Maxwell distribution. They then showed that the MD simulation would agree with MC simulations. This gives rise to BGK dynamics, a type of stochastic dynamics used by Montgomery, Chandler and Berne to simulate activated barrier crossing and later by Andersen in his canonical MD method. In BGK dynamics, exact Hamiltonian flow between collisions gives the canonical distribution, as first shown by Lebowitz and Bergmann. Unfortunately, when the equations of motion are integrated numerically, one cannot prove that the states sample the canonical distribution. Duane et al. [5] then introduced the Metropolis criterion for accepting or rejecting the momentum refreshed MD step. Their HMC does rigorously give the correct canonical distribution and is thus the method of choice.
    • (1995) J Chem Phys , vol.103 , pp. 8247-8256
    • Gromov, D.G.1    De Pablo, J.J.2
  • 40
    • 0000342374 scopus 로고
    • Hybrid Monte Carlo simulations of dense polymer system
    • Forrest BM, Suter UW: Hybrid Monte Carlo simulations of dense polymer system. J Chem Phys 1994, 101:2616-2029.
    • (1994) J Chem Phys , vol.101 , pp. 2616-12029
    • Forrest, B.M.1    Suter, U.W.2
  • 41
    • 0000342375 scopus 로고
    • Hybrid Monte Carlo simulation of polymer chains
    • Irbäck A: Hybrid Monte Carlo simulation of polymer chains. J Chem Phys 1994, 101:1661-1667.
    • (1994) J Chem Phys , vol.101 , pp. 1661-1667
    • Irbäck, A.1
  • 42
    • 0000088731 scopus 로고
    • An improved acceptance procedure for the Hybrid Monte Carlo algorithm
    • Neal RM: An improved acceptance procedure for the Hybrid Monte Carlo algorithm. J Comp Phys 1994, 111:194-203.
    • (1994) J Comp Phys , vol.111 , pp. 194-203
    • Neal, R.M.1
  • 43
    • 0001444302 scopus 로고
    • The acceptance probability in the Hybrid Monte Carlo method
    • Gupta S, Irbäck A, Karsch F, Petersson B: The acceptance probability in the Hybrid Monte Carlo method. Phys Lett B 1990, 242:437-443.
    • (1990) Phys Lett B , vol.242 , pp. 437-443
    • Gupta, S.1    Irbäck, A.2    Karsch, F.3    Petersson, B.4
  • 44
    • 0006660845 scopus 로고
    • An improved Hybrid Monte Carlo method
    • Mackenzie PB: An improved Hybrid Monte Carlo method. Phys Lett B 1989, 226:369-371.
    • (1989) Phys Lett B , vol.226 , pp. 369-371
    • Mackenzie, P.B.1
  • 45
    • 34547809547 scopus 로고
    • A unified formulation of the constant temperature molecular dynamic methods
    • Nosé S: A unified formulation of the constant temperature molecular dynamic methods. J Chem Phys 1984, 81:511-519.
    • (1984) J Chem Phys , vol.81 , pp. 511-519
    • Nosé, S.1
  • 46
    • 36448999094 scopus 로고
    • Efficient molecular dynamics and hybrid Monte Carlo algorithm for path integrals
    • Tuckerman M, Berne BJ, Martyna G, Klein M: Efficient molecular dynamics and hybrid Monte Carlo algorithm for path integrals. J Chem Phys 1993, 99:2796-2808.
    • (1993) J Chem Phys , vol.99 , pp. 2796-2808
    • Tuckerman, M.1    Berne, B.J.2    Martyna, G.3    Klein, M.4
  • 47
    • 36549099979 scopus 로고
    • Reducing quasi-ergodic behavior in Monte Carlo simulation by J-walking: Applications to atomic clusters
    • Frantz DD, Freeman DL, Doll JD: Reducing quasi-ergodic behavior in Monte Carlo simulation by J-walking: applications to atomic clusters. J Chem Phys 1990, 93:2769-2784.
    • (1990) J Chem Phys , vol.93 , pp. 2769-2784
    • Frantz, D.D.1    Freeman, D.L.2    Doll, J.D.3
  • 48
    • 36449008756 scopus 로고
    • Extending J-walking to quantum systems: Applications to atomic clusters
    • Frantz DD, Freeman DL, Doll JD: Extending J-walking to quantum systems: applications to atomic clusters. J Chem Phys 1992, 97:5713-5731.
    • (1992) J Chem Phys , vol.97 , pp. 5713-5731
    • Frantz, D.D.1    Freeman, D.L.2    Doll, J.D.3
  • 49
    • 0001751645 scopus 로고    scopus 로고
    • Computational study of the structures and thermodynamic properties of ammonium chloride clusters using a parallel jump-walking approach
    • Matro A, Freeman DL, Topper RQ: Computational study of the structures and thermodynamic properties of ammonium chloride clusters using a parallel jump-walking approach. J Chem Phys 1996, 104:8690-8702.
    • (1996) J Chem Phys , vol.104 , pp. 8690-8702
    • Matro, A.1    Freeman, D.L.2    Topper, R.Q.3
  • 50
    • 0002057815 scopus 로고    scopus 로고
    • Computational studies of clusters. Methods and results
    • Freeman DL, Doll JD: Computational studies of clusters. Methods and results. Annu Rev Phys Chem 1996, 47:43-80.
    • (1996) Annu Rev Phys Chem , vol.47 , pp. 43-80
    • Freeman, D.L.1    Doll, J.D.2
  • 51
    • 0013426912 scopus 로고
    • Gibbs free-energy changes for the growth of argon clusters adsorbed on graphite
    • Strozak MA, Lopez GE, Freeman DL: Gibbs free-energy changes for the growth of argon clusters adsorbed on graphite. J Chem Phys 1992, 97:4445-4452.
    • (1992) J Chem Phys , vol.97 , pp. 4445-4452
    • Strozak, M.A.1    Lopez, G.E.2    Freeman, D.L.3
  • 52
    • 0001754726 scopus 로고
    • A study of low temperature heat capacity anomalies in bimetallic alloy clusters using J-walking Monte Carlo methods
    • Lopez GE, Freeman DL: A study of low temperature heat capacity anomalies in bimetallic alloy clusters using J-walking Monte Carlo methods. J Chem Phys 1993, 98:1428-1435.
    • (1993) J Chem Phys , vol.98 , pp. 1428-1435
    • Lopez, G.E.1    Freeman, D.L.2
  • 53
    • 0001511584 scopus 로고
    • Methods for accelerating chain folding and mixing
    • Liu Z, Berne BJ: Methods for accelerating chain folding and mixing. J Chem Phys 1993, 99:6071-6077.
    • (1993) J Chem Phys , vol.99 , pp. 6071-6077
    • Liu, Z.1    Berne, B.J.2
  • 54
    • 0000106469 scopus 로고
    • Multicanonical algorithms for first order phase transitions
    • Berg BA, Neuhaus T: Multicanonical algorithms for first order phase transitions. Phys Lett B 1991, B267:249-253.
    • (1991) Phys Lett B , vol.B267 , pp. 249-253
    • Berg, B.A.1    Neuhaus, T.2
  • 55
    • 43949158791 scopus 로고
    • Comparative study of multicanonical and simulated annealing algorithms in the protein folding problem
    • Hansmann UHE, Okamoto Y: Comparative study of multicanonical and simulated annealing algorithms in the protein folding problem. Physica A 1994, 212:415-437.
    • (1994) Physica A , vol.212 , pp. 415-437
    • Hansmann, U.H.E.1    Okamoto, Y.2
  • 56
    • 0029342240 scopus 로고
    • Thermodynamics of helix-coil transitions studied by multicanonical algorithms
    • Okamoto Y, Hansmann UHE: Thermodynamics of helix-coil transitions studied by multicanonical algorithms. J Phys Chem 1995, 99:11276-11287 An application of multicanonical sampling to examine helix-coil transitions in isolated polypeptides ranging from 10-20 amino acids.
    • (1995) J Phys Chem , vol.99 , pp. 11276-11287
    • Okamoto, Y.1    Uhe, H.2
  • 57
    • 0000515198 scopus 로고
    • Monte Carlo simulation of a first-order transition for protein folding
    • Hao M-H, Scheraga HA: Monte Carlo simulation of a first-order transition for protein folding. J Phys Chem 1994, 98:4940-4948.
    • (1994) J Phys Chem , vol.98 , pp. 4940-4948
    • Hao, M.-H.1    Scheraga, H.A.2
  • 58
    • 33646516485 scopus 로고
    • Possible generalization of Boltzmann-Gibbs statistics
    • Tsallis C: Possible generalization of Boltzmann-Gibbs statistics. J Stat Phys 1988, 52:479-487.
    • (1988) J Stat Phys , vol.52 , pp. 479-487
    • Tsallis, C.1
  • 59
    • 0001205978 scopus 로고    scopus 로고
    • Generalized simulated annealing algorithms using Tsallis statistics: Application to conformational optimization of a tetrapeptide
    • Andricioaei I, Straub JE: Generalized simulated annealing algorithms using Tsallis statistics: application to conformational optimization of a tetrapeptide. Phys Rev E 1996, 53:R3055-R3058. A generalized MC algorithm that samples equilibrium Tsallis statistical distributions is presented. The relative efficiency of a simulated annealing protocol employing the generalized Monte Carlo algorithm is shown to be significantly more effective than MD or HMC based annealing algorithms in isolating the global energy minimum of a tetrapeptide.
    • (1996) Phys Rev E , vol.53
    • Andricioaei, I.1    Straub, J.E.2
  • 60
    • 84973610749 scopus 로고
    • A rapidly convergent simulation method: Mixed Monte Carlo/stochastic dynamics
    • Guarnieri F, Still WC: A rapidly convergent simulation method: Mixed Monte Carlo/stochastic dynamics. J Comp Chem 1994, 11:1302-1310.
    • (1994) J Comp Chem , vol.11 , pp. 1302-1310
    • Guarnieri, F.1    Still, W.C.2
  • 61
    • 0000167458 scopus 로고
    • A smart Monte Carlo technique for free energy simulations of multiconformational molecules. Direct calculations of the conformational populations of organic molecules
    • Senderowitz H, Guarnieri F, Still, WC: A smart Monte Carlo technique for free energy simulations of multiconformational molecules. Direct calculations of the conformational populations of organic molecules. J Am Chem Soc 1995, 117:8211-8219.
    • (1995) J Am Chem Soc , vol.117 , pp. 8211-8219
    • Senderowitz, H.1    Guarnieri, F.2    Still, W.C.3
  • 62
    • 0001629697 scopus 로고
    • Cluster optimization simplified by interaction modification
    • Stillinger FH, Stillinger DK: Cluster optimization simplified by interaction modification. J Chem Phys 1990, 93:6106-6107.
    • (1990) J Chem Phys , vol.93 , pp. 6106-6107
    • Stillinger, F.H.1    Stillinger, D.K.2
  • 63
    • 0027551825 scopus 로고
    • Predicting polypeptide and protein structures from amino acid sequence: Antlion method applied to melittin
    • Head-Gordon T, Stillinger FH: Predicting polypeptide and protein structures from amino acid sequence: Antlion method applied to melittin. Biopolymers 1993, 33:293-303.
    • (1993) Biopolymers , vol.33 , pp. 293-303
    • Head-Gordon, T.1    Stillinger, F.H.2
  • 64
    • 0000594925 scopus 로고
    • The multiple-minima problem in the conformational analysis of molecules. Deformation of the potential energy hypersurface by the Diffusion Equation Method
    • Piela L, Kostrowicki J, Scheraga HA: The multiple-minima problem in the conformational analysis of molecules. Deformation of the potential energy hypersurface by the Diffusion Equation Method. J Phys Chem 1989, 93:3339-3346.
    • (1989) J Phys Chem , vol.93 , pp. 3339-3346
    • Piela, L.1    Kostrowicki, J.2    Scheraga, H.A.3
  • 65
    • 0001031118 scopus 로고
    • Application of the Diffusion Equation Method for global optimization to oligopeptides
    • Kostrowicki J, Scheraga HA: Application of the Diffusion Equation Method for global optimization to oligopeptides. J Phys Chem 1992, 96:7442-7449.
    • (1992) J Phys Chem , vol.96 , pp. 7442-7449
    • Kostrowicki, J.1    Scheraga, H.A.2
  • 66
    • 0342453492 scopus 로고    scopus 로고
    • Some approaches to the multiple-minima problem in protein folding
    • Edited by Pardalos PM, Shalloway D, Xue G. Providence: American Mathematical Society
    • Kostrowicki J, Scheraga HA: Some approaches to the multiple-minima problem in protein folding. In Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding. Edited by Pardalos PM, Shalloway D, Xue G. Providence: American Mathematical Society; 1996:123-132. A discussion of methods for extending the DEM to internal coordinates (dihedral-angle space) is presented.
    • (1996) Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding , pp. 123-132
    • Kostrowicki, J.1    Scheraga, H.A.2
  • 67
    • 0002251853 scopus 로고
    • Edited by Floudas CA, Pardalos PM. Princeton: Princeton University Press
    • Shalloway D: Recent advances in global optimization. Edited by Floudas CA, Pardalos PM. Princeton: Princeton University Press; 1992:433-477.
    • (1992) Recent Advances in Global Optimization , pp. 433-477
    • Shalloway, D.1
  • 68
    • 0042754937 scopus 로고    scopus 로고
    • Tracking metastable states to free-energy global minima
    • Edited by Pardalos PM, Shalloway D, Xue G. American Mathematical Society; Providence
    • Church BW, Orešič M, Shalloway D: Tracking metastable states to free-energy global minima. In Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding. Edited by Pardalos PM, Shalloway D, Xue G. American Mathematical Society; Providence; 1996:41-64. This paper provides and excellent introduction to the PA method. The PA method is related to a reduced Smoluchowski diffusion equation making an intriguing connection to diffusive kinetics between conformational substates. Application of the PA method to Met-enkephalin is described as a means of gaining insight into the pathways available to peptides and proteins during annealing or folding.
    • (1996) Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding , pp. 41-64
    • Church, B.W.1    Orešič, M.2    Shalloway, D.3
  • 69
    • 4944265163 scopus 로고
    • Global energy minimum searches using an approximate solution of the imaginary time Schrödinger equation
    • Amara P, Hsu D, Straub JE: Global energy minimum searches using an approximate solution of the imaginary time Schrödinger equation. J Phys Chem 1993, 97:6715-6721.
    • (1993) J Phys Chem , vol.97 , pp. 6715-6721
    • Amara, P.1    Hsu, D.2    Straub, J.E.3
  • 70
    • 36449003371 scopus 로고
    • Approximate solution of the classical Liouville equation using Gaussian phase packet dynamics: Application to enhanced equilibrium averaging and global optimization
    • Ma J, Hsu D, Straub JE: Approximate solution of the classical Liouville equation using Gaussian phase packet dynamics: application to enhanced equilibrium averaging and global optimization. J Chem Phys 1993, 49:4024-4035.
    • (1993) J Chem Phys , vol.49 , pp. 4024-4035
    • Ma, J.1    Hsu, D.2    Straub, J.E.3
  • 71
    • 0002623852 scopus 로고    scopus 로고
    • Optimization techniques with applications to proteins
    • Edited by Elber R. Singapore: World Scientific
    • Straub JE: Optimization techniques with applications to proteins. In Recent Developments in Theoretical Studies of Proteins. Edited by Elber R. Singapore: World Scientific; 1996:137-196. This review presents a complete overview of potential-smoothing algorithms applied to global energy minimization of biomolecular systems.
    • (1996) Recent Developments in Theoretical Studies of Proteins , pp. 137-196
    • Straub, J.E.1
  • 72
    • 0001083082 scopus 로고
    • Folding model proteins using kinetic and thermodynamic annealing of the classical density distribution
    • Amara P, Straub JE: Folding model proteins using kinetic and thermodynamic annealing of the classical density distribution. J Phys Chem 1995, 99:14840-14852. This paper presents a study of global energy minimization for a series of model proteins using simulated annealing and potential-smoothing algorithms. A critical evaluation of Gaussian potential-smoothing methods and a comparison with MD simulated annealing is presented.
    • (1995) J Phys Chem , vol.99 , pp. 14840-14852
    • Amara, P.1    Straub, J.E.2
  • 73
    • 36449006131 scopus 로고
    • Modeling side chains in peptides and proteins: Application of the locally enhanced sampling and the simulated annealing methods to find minimum energy conformations
    • Roitberg A, Elber R: Modeling side chains in peptides and proteins: application of the locally enhanced sampling and the simulated annealing methods to find minimum energy conformations. J Chem Phys 1991, 95:9277-9287.
    • (1991) J Chem Phys , vol.95 , pp. 9277-9287
    • Roitberg, A.1    Elber, R.2
  • 74
    • 0004162305 scopus 로고
    • Locally enhanced sampling in free energy calculations: Application of mean field approximation to accurate calculation of free energy differences
    • Verkhivker G, Elber R, Nowak W: Locally enhanced sampling in free energy calculations: application of mean field approximation to accurate calculation of free energy differences. J Chem Phys 1992, 97:7838-7841.
    • (1992) J Chem Phys , vol.97 , pp. 7838-7841
    • Verkhivker, G.1    Elber, R.2    Nowak, W.3
  • 75
    • 0001276588 scopus 로고
    • Quantum annealing: A new method for minimizing multidimensional functions
    • Finnila AB, Gomez MA, Sebenik C, Stenson C, Doll JD: Quantum annealing: a new method for minimizing multidimensional functions. Chem Phys Lett 1994, 219:343-348.
    • (1994) Chem Phys Lett , vol.219 , pp. 343-348
    • Finnila, A.B.1    Ma, G.2    Sebenik, C.3    Stenson, C.4    Doll, J.D.5
  • 76
    • 0030245249 scopus 로고    scopus 로고
    • Finding the needle in the haystack: Algorithms for conformational optimization
    • Andricioaei I, Straub JE: Finding the needle in the haystack: algorithms for conformational optimization. Comput Phys 1996, 10:449-454. This tutorial introduction to molecular conformational optimization presents an overview of simulated annealing, Gaussian potential smoothing, quantum mechanical annealing and the Method of Bad Derivatives.
    • (1996) Comput Phys , vol.10 , pp. 449-454
    • Andricioaei, I.1    Straub, J.E.2


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