메뉴 건너뛰기




Volumn 2, Issue 5, 2012, Pages 771-779

New advances in metadynamics

Author keywords

[No Author keywords available]

Indexed keywords


EID: 84865279536     PISSN: 17590876     EISSN: 17590884     Source Type: Journal    
DOI: 10.1002/wcms.1103     Document Type: Article
Times cited : (158)

References (68)
  • 1
    • 36849039429 scopus 로고    scopus 로고
    • A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
    • Henzler-Wildman K, Lei M, Thai V, Kerns S, Karplus M, Kern D. A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 2007, 450:913-916.
    • (2007) Nature , vol.450 , pp. 913-916
    • Henzler-Wildman, K.1    Lei, M.2    Thai, V.3    Kerns, S.4    Karplus, M.5    Kern, D.6
  • 3
    • 4243661501 scopus 로고
    • Constrained reaction coordinate dynamics for the simulation of rare events
    • Carter EA, 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.A.1    Ciccotti, G.2    Hynes, J.T.3    Kapral, R.4
  • 5
    • 0001060458 scopus 로고
    • Monte-carlo method for obtaining interionic potential of mean force in ionic solution
    • Patey GN, Valleau JP. Monte-carlo method for obtaining interionic potential of mean force in ionic solution. J Chem Phys 1975, 63:2334-2339.
    • (1975) J Chem Phys , vol.63 , pp. 2334-2339
    • Patey, G.N.1    Valleau, J.P.2
  • 6
    • 0000689085 scopus 로고
    • Predicting slow structural transitions in macromolecular systems: conformational flooding
    • 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
    • Grubmüller, H.1
  • 7
    • 33646987405 scopus 로고
    • Optimized Monte Carlo data analysis
    • Ferrenberg A, Swendsen R. Optimized Monte Carlo data analysis. Phys Rev Lett 1989, 63:1195-1198.
    • (1989) Phys Rev Lett , vol.63 , pp. 1195-1198
    • Ferrenberg, A.1    Swendsen, R.2
  • 8
    • 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.
    • (1997) Phys Rev Lett , vol.78 , pp. 2690
    • Jarzynski, C.1
  • 9
    • 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
  • 10
    • 0042852135 scopus 로고    scopus 로고
    • Reconstructing potentials of mean force through time series analysis of steered molecular dynamics simulations
    • Gullingsrud J, Braun R, Schulten K. Reconstructing potentials of mean force through time series analysis of steered molecular dynamics simulations. J Comput Phys 1999, 151:190-211.
    • (1999) J Comput Phys , vol.151 , pp. 190-211
    • Gullingsrud, J.1    Braun, R.2    Schulten, K.3
  • 11
    • 0028710015 scopus 로고
    • Local elevation: a method for improving the searching properties of molecular dynamics simulation
    • Huber T, Torda A, van Gunsteren W. 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.2    van Gunsteren, W.3
  • 12
    • 0037085922 scopus 로고    scopus 로고
    • On the use of the adiabatic molecular dynamics technique in the calculation of free energy profiles
    • Rosso L, Minary P, Zhu Z, Tuckerman M. On the use of the adiabatic molecular dynamics technique in the calculation of free energy profiles. J Comput Phys 2002, 116:4389-4402.
    • (2002) J Comput Phys , vol.116 , pp. 4389-4402
    • Rosso, L.1    Minary, P.2    Zhu, Z.3    Tuckerman, M.4
  • 14
    • 38349091489 scopus 로고    scopus 로고
    • Well-tempered metadynamics: a smoothly converging and tunable free-energy method
    • Barducci A, Bussi G, Parrinello M. Well-tempered metadynamics: a smoothly converging and tunable free-energy method. Phys Rev Lett 2008, 100:20603-4.
    • (2008) Phys Rev Lett , vol.100 , pp. 20603-20604
    • Barducci, A.1    Bussi, G.2    Parrinello, M.3
  • 15
    • 58149299971 scopus 로고    scopus 로고
    • Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
    • Laio A, Gervasio F. Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science. Rep Prog Phys 2008, 71:126601.
    • (2008) Rep Prog Phys , vol.71 , pp. 126601
    • Laio, A.1    Gervasio, F.2
  • 19
    • 46249092554 scopus 로고    scopus 로고
    • GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation
    • Hess B, Kutzner C, van der Spoel D, Lindahl E. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 2008, 4:435-447.
    • (2008) J Chem Theory Comput , vol.4 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    van der Spoel, D.3    Lindahl, E.4
  • 20
    • 67650099787 scopus 로고    scopus 로고
    • ACEMD: accelerating Biomolecular Dynamics in the Microsecond Time Scale
    • Harvey MJ, Giupponi G, Fabritiis GD. ACEMD: accelerating Biomolecular Dynamics in the Microsecond Time Scale. J Chem Theory Comput 2009, 5:1632-1639.
    • (2009) J Chem Theory Comput , vol.5 , pp. 1632-1639
    • Harvey, M.J.1    Giupponi, G.2    Fabritiis, G.D.3
  • 22
    • 33644772083 scopus 로고    scopus 로고
    • Equilibrium free energies from nonequilibrium metadynamics
    • Bussi G, Laio A, Parrinello M. Equilibrium free energies from nonequilibrium metadynamics. Phys Rev Lett 2006, 96:090601.
    • (2006) Phys Rev Lett , vol.96 , pp. 090601
    • Bussi, G.1    Laio, A.2    Parrinello, M.3
  • 24
    • 33746900781 scopus 로고    scopus 로고
    • Self-healing umbrella sampling: a non-equilibrium approach for quantitative free energy calculations
    • Marsili S, Barducci A, Chelli R, Procacci P, Schettino V. Self-healing umbrella sampling: a non-equilibrium approach for quantitative free energy calculations. J Phys Chem B 2006, 110:14011-14013.
    • (2006) J Phys Chem B , vol.110 , pp. 14011-14013
    • Marsili, S.1    Barducci, A.2    Chelli, R.3    Procacci, P.4    Schettino, V.5
  • 25
    • 21244439384 scopus 로고    scopus 로고
    • The role of the peripheral anionic site and cation-pi interactions in the ligand penetration of the human AChE gorge
    • Branduardi D, Gervasio FL, Cavalli A, Recantini M, Parrinello M. The role of the peripheral anionic site and cation-pi interactions in the ligand penetration of the human AChE gorge. J Am Chem Soc 2005, 127:9147-9155.
    • (2005) J Am Chem Soc , vol.127 , pp. 9147-9155
    • Branduardi, D.1    Gervasio, F.L.2    Cavalli, A.3    Recantini, M.4    Parrinello, M.5
  • 26
    • 67549127330 scopus 로고    scopus 로고
    • On the calculation of puckering free energy surfaces
    • Sega M, Autieri E, Pederiva F. On the calculation of puckering free energy surfaces. J Chem Phys 2009, 130:225102.
    • (2009) J Chem Phys , vol.130 , pp. 225102
    • Sega, M.1    Autieri, E.2    Pederiva, F.3
  • 27
    • 73349098763 scopus 로고    scopus 로고
    • A collective variable for the efficient exploration of protein beta-sheet structures: application to SH3 and GB1
    • Pietrucci F, Laio A. A collective variable for the efficient exploration of protein beta-sheet structures: application to SH3 and GB1. J Chem Theory Comput 2009, 5:2197-2201.
    • (2009) J Chem Theory Comput , vol.5 , pp. 2197-2201
    • Pietrucci, F.1    Laio, A.2
  • 29
    • 33750040264 scopus 로고    scopus 로고
    • Free-energy landscape for hairpin folding from combined parallel tempering and metadynamics
    • Bussi G, Gervasio FL, Laio A, Parrinello M. Free-energy landscape for hairpin folding from combined parallel tempering and metadynamics. J Am Chem Soc 2006, 128:13425-13441.
    • (2006) J Am Chem Soc , vol.128 , pp. 13425-13441
    • Bussi, G.1    Gervasio, F.L.2    Laio, A.3    Parrinello, M.4
  • 30
    • 77951585445 scopus 로고    scopus 로고
    • Metadynamics as a tool for mapping the con- formational and free-energy space of peptides-the alanine dipeptide case study
    • Vymetal J, Vondrasek J. Metadynamics as a tool for mapping the con- formational and free-energy space of peptides-the alanine dipeptide case study. J Phys Chem B 2010, 114:5632-5642.
    • (2010) J Phys Chem B , vol.114 , pp. 5632-5642
    • Vymetal, J.1    Vondrasek, J.2
  • 31
    • 84859756922 scopus 로고    scopus 로고
    • Graph theory meets ab initio molecular dynamics: atomic structures and transformations at the nanoscale
    • Pietrucci F, Andreoni W. Graph theory meets ab initio molecular dynamics: atomic structures and transformations at the nanoscale. Phys Rev Lett 2011, 107:085504.
    • (2011) Phys Rev Lett , vol.107 , pp. 085504
    • Pietrucci, F.1    Andreoni, W.2
  • 32
    • 54249091171 scopus 로고    scopus 로고
    • The unfolded ensemble and folding mechanism of the C-terminal GB1 β-hairpin
    • Bonomi M, Branduardi D, Gervasio F, Parrinello M. The unfolded ensemble and folding mechanism of the C-terminal GB1 β-hairpin. J Am Chem Soc 2008, 130:13938-13944.
    • (2008) J Am Chem Soc , vol.130 , pp. 13938-13944
    • Bonomi, M.1    Branduardi, D.2    Gervasio, F.3    Parrinello, M.4
  • 33
    • 79959770147 scopus 로고    scopus 로고
    • A chirality-based metrics for free-energy calculations in biomolecular systems
    • Pietropaolo A, Branduardi D, Bonomi M, Parrinello M. A chirality-based metrics for free-energy calculations in biomolecular systems. J Comput Chem 2011, 32:2627-2637.
    • (2011) J Comput Chem , vol.32 , pp. 2627-2637
    • Pietropaolo, A.1    Branduardi, D.2    Bonomi, M.3    Parrinello, M.4
  • 35
    • 78651327755 scopus 로고    scopus 로고
    • Comparing the efficiency of biased and unbiased molecular dynamics in reconstructing the free energy landscape of met-enkephalin
    • Sutto L, D'Abramo M, Luigi Gervasio F. Comparing the efficiency of biased and unbiased molecular dynamics in reconstructing the free energy landscape of met-enkephalin. J Chem Theory Comput 2010, 6:3640-3646.
    • (2010) J Chem Theory Comput , vol.6 , pp. 3640-3646
    • Sutto, L.1    D'Abramo, M.2    Luigi Gervasio, F.3
  • 36
    • 34147097967 scopus 로고    scopus 로고
    • Metadynamics in essential coordinates: free energy simulation of conformational changes
    • Spiwok V, Lipovov́a P, Kralov́a B. Metadynamics in essential coordinates: free energy simulation of conformational changes. J Phys Chem B 2007, 111:3073-3076.
    • (2007) J Phys Chem B , vol.111 , pp. 3073-3076
    • Spiwok, V.1    Lipovov́a, P.2    Kralov́a, B.3
  • 37
    • 53149099307 scopus 로고    scopus 로고
    • Continuous metadynamics in essential coordinates as a tool for free energy modeling of conformational changes
    • Spiwok V, Králov́a B, Tvaroska I. Continuous metadynamics in essential coordinates as a tool for free energy modeling of conformational changes. J Mol Model 2008, 14:995-1002.
    • (2008) J Mol Model , vol.14 , pp. 995-1002
    • Spiwok, V.1    Králov́a, B.2    Tvaroska, I.3
  • 38
    • 83755206813 scopus 로고    scopus 로고
    • Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap
    • Spiwok V, Králov́a B. Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap. J Chem Phys 2011, 135, 224504.
    • (2011) J Chem Phys , vol.135 , pp. 224504
    • Spiwok, V.1    Králov́a, B.2
  • 39
    • 0034704229 scopus 로고    scopus 로고
    • A global geometric framework for nonlinear dimensionality reduction
    • Tenenbaum J, de Silva V, Langford J. A global geometric framework for nonlinear dimensionality reduction. Science 2000, 290:2319-2323.
    • (2000) Science , vol.290 , pp. 2319-2323
    • Tenenbaum, J.1    de Silva, V.2    Langford, J.3
  • 40
    • 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
  • 41
    • 0037305918 scopus 로고    scopus 로고
    • Multiplexed-replica exchange molecular dynamics method for protein folding simulation
    • Rhee YM, Pande VS. Multiplexed-replica exchange molecular dynamics method for protein folding simulation. Biophys J 2003, 84:775-786.
    • (2003) Biophys J , vol.84 , pp. 775-786
    • Rhee, Y.M.1    Pande, V.S.2
  • 43
    • 33644772083 scopus 로고    scopus 로고
    • Equilibrium free energies from nonequilibrium metadynamics
    • Bussi G, Laio A, Parrinello M. Equilibrium free energies from nonequilibrium metadynamics. Phys Rev Lett 2006, 96:090601.
    • (2006) Phys Rev Lett , vol.96 , pp. 090601
    • Bussi, G.1    Laio, A.2    Parrinello, M.3
  • 44
    • 79959204416 scopus 로고    scopus 로고
    • Assessing the quality of the OPEP coarse-grained force field
    • Barducci A, Bonomi M, Derreumaux P. Assessing the quality of the OPEP coarse-grained force field. J Chem Theory Comput 2011, 7:1928-1934.
    • (2011) J Chem Theory Comput , vol.7 , pp. 1928-1934
    • Barducci, A.1    Bonomi, M.2    Derreumaux, P.3
  • 46
    • 84856694630 scopus 로고    scopus 로고
    • The different flexibility of c-Src and c-Abl kinases regulates the accessibility of a druggable inactive conformation
    • Lovera S, Sutto L, Boubeva R, Scapozza L, Dölker N, Gervasio F. The different flexibility of c-Src and c-Abl kinases regulates the accessibility of a druggable inactive conformation. J Am Chem Soc 2012, 134:2496-2499.
    • (2012) J Am Chem Soc , vol.134 , pp. 2496-2499
    • Lovera, S.1    Sutto, L.2    Boubeva, R.3    Scapozza, L.4    Dölker, N.5    Gervasio, F.6
  • 47
  • 48
    • 79952267622 scopus 로고    scopus 로고
    • Finite temperature properties of clusters by replica exchange metadynamics: the water nonamer
    • Zhai Y, Laio A, Tosatti E, Gong XG. Finite temperature properties of clusters by replica exchange metadynamics: the water nonamer. J Am Chem Soc 2011, 133:2535-2540.
    • (2011) J Am Chem Soc , vol.133 , pp. 2535-2540
    • Zhai, Y.1    Laio, A.2    Tosatti, E.3    Gong, X.G.4
  • 49
    • 78650809380 scopus 로고    scopus 로고
    • Multicanonical molecular dynamics simulations combined with metadynamics for the free energy landscape of a biomolecular system with high energy barriers
    • Yonezawa Y, Shimoyama H, Nakamura H. Multicanonical molecular dynamics simulations combined with metadynamics for the free energy landscape of a biomolecular system with high energy barriers. Chem Phys Lett 2011, 501:598-602.
    • (2011) Chem Phys Lett , vol.501 , pp. 598-602
    • Yonezawa, Y.1    Shimoyama, H.2    Nakamura, H.3
  • 50
    • 77952404209 scopus 로고    scopus 로고
    • Enhanced sampling in the well-tempered ensemble
    • Bonomi M, Parrinello M. Enhanced sampling in the well-tempered ensemble. Phys Rev Lett 2010, 104:190601-190604.
    • (2010) Phys Rev Lett , vol.104 , pp. 190601-190604
    • Bonomi, M.1    Parrinello, M.2
  • 51
    • 34249071886 scopus 로고    scopus 로고
    • A bias-exchange approach to protein folding
    • Piana S, Laio A. A bias-exchange approach to protein folding. J Phys Chem B 2007, 111:4553-4559.
    • (2007) J Phys Chem B , vol.111 , pp. 4553-4559
    • Piana, S.1    Laio, A.2
  • 52
    • 83455244845 scopus 로고    scopus 로고
    • A hybrid all-atom structure-based model for protein folding and large scale conformational transitions
    • Sutto L, Mereu I, Gervasio FL. A hybrid all-atom structure-based model for protein folding and large scale conformational transitions. J Chem Theory Comput 2011, 7:4208-4217.
    • (2011) J Chem Theory Comput , vol.7 , pp. 4208-4217
    • Sutto, L.1    Mereu, I.2    Gervasio, F.L.3
  • 53
    • 84855765478 scopus 로고    scopus 로고
    • Conformational selection versus induced fit in kinases: the case of PI3K-γ
    • D'Abramo M, Rabal O, Oyarzabal J, Gervasio FL. Conformational selection versus induced fit in kinases: the case of PI3K-γ. Angew Chem Int Ed 2012, 51:642-646.
    • (2012) Angew Chem Int Ed , vol.51 , pp. 642-646
    • D'Abramo, M.1    Rabal, O.2    Oyarzabal, J.3    Gervasio, F.L.4
  • 54
    • 69049084558 scopus 로고    scopus 로고
    • Substrate binding mechanism of HIV-1 protease from explicit-solvent atomistic simulations
    • Pietrucci F, Marinelli F, Carloni P, Laio A. Substrate binding mechanism of HIV-1 protease from explicit-solvent atomistic simulations. J Am Chem Soc 2009, 131:11811-11818.
    • (2009) J Am Chem Soc , vol.131 , pp. 11811-11818
    • Pietrucci, F.1    Marinelli, F.2    Carloni, P.3    Laio, A.4
  • 55
    • 79960220436 scopus 로고    scopus 로고
    • Combined Metadynamics and umbrella sampling method for the calculation of ion permeation free energy profiles
    • Zhang Y, Voth GA. Combined Metadynamics and umbrella sampling method for the calculation of ion permeation free energy profiles. J Chem Theory Comput 2011, 7:2277-2283.
    • (2011) J Chem Theory Comput , vol.7 , pp. 2277-2283
    • Zhang, Y.1    Voth, G.A.2
  • 56
    • 0001692244 scopus 로고    scopus 로고
    • Lambda-dynamics: a new approach to free energy calculations
    • Kong X, Brooks CL. Lambda-dynamics: a new approach to free energy calculations. J Chem Phys 1996, 105:2414.
    • (1996) J Chem Phys , vol.105 , pp. 2414
    • Kong, X.1    Brooks, C.L.2
  • 57
    • 80052344755 scopus 로고    scopus 로고
    • Lambda-metadynamics approach to compute absolute solvation free energy
    • Wu P, Hu X, Yang W. Lambda-metadynamics approach to compute absolute solvation free energy. J Phys Chem Lett 2011, 2:2099-2103.
    • (2011) J Phys Chem Lett , vol.2 , pp. 2099-2103
    • Wu, P.1    Hu, X.2    Yang, W.3
  • 58
    • 52949137003 scopus 로고    scopus 로고
    • Diffusive reaction dynamics on invariant free energy profiles
    • Krivov SV, M K. Diffusive reaction dynamics on invariant free energy profiles. Proc Natl Acad Sci USA 2008, 105:13841-13846.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 13841-13846
    • Krivov, S.V.1    M, K.2
  • 59
    • 81755171988 scopus 로고    scopus 로고
    • Flux tempered metadynamics
    • Singh S, Chiu Cc, Pablo JJ. Flux tempered metadynamics. J Stat Phys 2011, 145:932-945.
    • (2011) J Stat Phys , vol.145 , pp. 932-945
    • Singh, S.1    Chiu, C.2    Pablo, J.J.3
  • 60
    • 41349094233 scopus 로고    scopus 로고
    • Optimizing the ensemble for equilibration in broad-histogram Monte Carlo simulations
    • Trebst A, Huse DA, Troyer M. Optimizing the ensemble for equilibration in broad-histogram Monte Carlo simulations. Phys Rev E 2004, 70:046701.
    • (2004) Phys Rev E , vol.70 , pp. 046701
    • Trebst, A.1    Huse, D.A.2    Troyer, M.3
  • 63
    • 80051959824 scopus 로고    scopus 로고
    • Simplifying the representation of complex free-energy landscapes using sketch-map
    • Ceriotti M, Tribello G, Parrinello M. Simplifying the representation of complex free-energy landscapes using sketch-map. Proc Natl Acad Sci USA 2011, 108:13023-13028.
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 13023-13028
    • Ceriotti, M.1    Tribello, G.2    Parrinello, M.3
  • 64
    • 67650477115 scopus 로고    scopus 로고
    • Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics
    • Bonomi M, Barducci A, Parrinello M. Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics. J Comput Chem 2009, 30:1615-1621.
    • (2009) J Comput Chem , vol.30 , pp. 1615-1621
    • Bonomi, M.1    Barducci, A.2    Parrinello, M.3
  • 65
    • 80055015114 scopus 로고    scopus 로고
    • METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations
    • Biarńes X, Pietrucci F, Marinelli F, Laio A. METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations. Comput Phys Commun 2012, 183:203-211.
    • (2012) Comput Phys Commun , vol.183 , pp. 203-211
    • Biarńes, X.1    Pietrucci, F.2    Marinelli, F.3    Laio, A.4
  • 66


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.