메뉴 건너뛰기




Volumn 10, Issue 7, 2014, Pages 2677-2689

Improved reweighting of accelerated molecular dynamics simulations for free energy calculation

Author keywords

[No Author keywords available]

Indexed keywords


EID: 84904131589     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct500090q     Document Type: Article
Times cited : (341)

References (46)
  • 1
    • 3142716857 scopus 로고    scopus 로고
    • Accelerated Molecular Dynamics: A Promising and Efficient Simulation Method for Biomolecules
    • Hamelberg, D.; Mongan, J.; McCammon, J. A. Accelerated Molecular Dynamics: A Promising and Efficient Simulation Method for Biomolecules J. Chem. Phys. 2004, 120 (24) 11919-11929
    • (2004) J. Chem. Phys. , vol.120 , Issue.24 , pp. 11919-11929
    • Hamelberg, D.1    Mongan, J.2    McCammon, J.A.3
  • 2
    • 38449096891 scopus 로고    scopus 로고
    • Sampling of Slow Diffusive Conformational Transitions with Accelerated Molecular Dynamics
    • Hamelberg, D.; de Oliveira, C. A. F.; McCammon, J. A. Sampling of Slow Diffusive Conformational Transitions with Accelerated Molecular Dynamics J. Chem. Phys. 2007, 127 (15) 155102
    • (2007) J. Chem. Phys. , vol.127 , Issue.15 , pp. 155102
    • Hamelberg, D.1    De Oliveira, C.A.F.2    McCammon, J.A.3
  • 3
    • 84861210523 scopus 로고    scopus 로고
    • Nucleotide-Dependent Mechanism of Get3 As Elucidated from Free Energy Calculations
    • Wereszczynski, J.; McCammon, J. A. Nucleotide-Dependent Mechanism of Get3 As Elucidated from Free Energy Calculations Proc. Natl. Acad. Sci. U.S.A. 2012, 109 (20) 7759-7764
    • (2012) Proc. Natl. Acad. Sci. U.S.A. , vol.109 , Issue.20 , pp. 7759-7764
    • Wereszczynski, J.1    McCammon, J.A.2
  • 5
    • 79952936165 scopus 로고    scopus 로고
    • Adaptive Accelerated Molecular Dynamics (Ad-AMD) Revealing the Molecular Plasticity of P450cam
    • Markwick, P. R. L.; Pierce, L. C. T.; Goodin, D. B.; McCammon, J. A. Adaptive Accelerated Molecular Dynamics (Ad-AMD) Revealing the Molecular Plasticity of P450cam J. Phys. Chem. Lett. 2011, 2 (3) 158-164
    • (2011) J. Phys. Chem. Lett. , vol.2 , Issue.3 , pp. 158-164
    • Markwick, P.R.L.1    Pierce, L.C.T.2    Goodin, D.B.3    McCammon, J.A.4
  • 6
    • 79955560141 scopus 로고    scopus 로고
    • Accessing a Hidden Conformation of the Maltose Binding Protein Using Accelerated Molecular Dynamics
    • Bucher, D.; Grant, B. J.; Markwick, P. R.; McCammon, J. A. Accessing a Hidden Conformation of the Maltose Binding Protein Using Accelerated Molecular Dynamics PLoS Comput. Biol. 2011, 7 (4) e1002034
    • (2011) PLoS Comput. Biol. , vol.7 , Issue.4 , pp. 1002034
    • Bucher, D.1    Grant, B.J.2    Markwick, P.R.3    McCammon, J.A.4
  • 10
    • 84892531306 scopus 로고    scopus 로고
    • Mapping of Allosteric Druggable Sites in Activation-Associated Conformers of the M2Muscarinic Receptor
    • Miao, Y.; Nichols, S. E.; McCammon, J. A. Mapping of Allosteric Druggable Sites in Activation-Associated Conformers of the M2Muscarinic Receptor Chem. Biol. Drug Des. 2013, 83 (2) 237-246
    • (2013) Chem. Biol. Drug Des. , vol.83 , Issue.2 , pp. 237-246
    • Miao, Y.1    Nichols, S.E.2    McCammon, J.A.3
  • 11
    • 47849086387 scopus 로고    scopus 로고
    • A Statistical Analysis of the Precision of Reweighting-Based Simulations
    • Shen, T. Y.; Hamelberg, D. A Statistical Analysis of the Precision of Reweighting-Based Simulations J. Chem. Phys. 2008, 129 (3) 034103
    • (2008) J. Chem. Phys. , vol.129 , Issue.3 , pp. 034103
    • Shen, T.Y.1    Hamelberg, D.2
  • 12
    • 81255138340 scopus 로고    scopus 로고
    • Studying functional dynamics in bio-molecules using accelerated molecular dynamics
    • Markwick, P. R. L.; McCammon, J. A. Studying functional dynamics in bio-molecules using accelerated molecular dynamics Phys. Chem. Chem. Phys. 2011, 13 (45) 20053-20065
    • (2011) Phys. Chem. Chem. Phys. , vol.13 , Issue.45 , pp. 20053-20065
    • Markwick, P.R.L.1    McCammon, J.A.2
  • 13
    • 84896351138 scopus 로고    scopus 로고
    • Free Energy Landscape of G-Protein Coupled Receptors, Explored by Accelerated Molecular Dynamics
    • Miao, Y.; Nichols, S. E.; McCammon, J. A. Free Energy Landscape of G-Protein Coupled Receptors, Explored by Accelerated Molecular Dynamics Phys. Chem. Chem. Phys. 2014, 16 (14) 6398-6406
    • (2014) Phys. Chem. Chem. Phys. , vol.16 , Issue.14 , pp. 6398-6406
    • Miao, Y.1    Nichols, S.E.2    McCammon, J.A.3
  • 14
    • 84886676069 scopus 로고    scopus 로고
    • Population Based Reweighting of Scaled Molecular Dynamics
    • Sinko, W.; Miao, Y.; de Oliveira, C. A. F.; McCammon, J. A. Population Based Reweighting of Scaled Molecular Dynamics J. Phys. Chem. B 2013, 117 (42) 12759-12768
    • (2013) J. Phys. Chem. B , vol.117 , Issue.42 , pp. 12759-12768
    • Sinko, W.1    Miao, Y.2    De Oliveira, C.A.F.3    McCammon, J.A.4
  • 15
    • 78149458812 scopus 로고    scopus 로고
    • Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations
    • Wereszczynski, J.; McCammon, J. A. Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations J. Chem. Theory Comput. 2010, 6 (11) 3285-3292
    • (2010) J. Chem. Theory Comput. , vol.6 , Issue.11 , pp. 3285-3292
    • Wereszczynski, J.1    McCammon, J.A.2
  • 16
    • 58149159707 scopus 로고    scopus 로고
    • Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration
    • Fajer, M.; Hamelberg, D.; McCammon, J. A. Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration J. Chem. Theory Comput. 2008, 4 (10) 1565-1569
    • (2008) J. Chem. Theory Comput. , vol.4 , Issue.10 , pp. 1565-1569
    • Fajer, M.1    Hamelberg, D.2    McCammon, J.A.3
  • 17
    • 67650498345 scopus 로고    scopus 로고
    • Using Multistate Free Energy Techniques to Improve the Efficiency of Replica Exchange Accelerated Molecular Dynamics
    • Fajer, M.; Swift, R. V.; McCammon, J. A. Using Multistate Free Energy Techniques to Improve the Efficiency of Replica Exchange Accelerated Molecular Dynamics J. Comput. Chem. 2009, 30 (11) 1719-1725
    • (2009) J. Comput. Chem. , vol.30 , Issue.11 , pp. 1719-1725
    • Fajer, M.1    Swift, R.V.2    McCammon, J.A.3
  • 18
    • 84872168026 scopus 로고    scopus 로고
    • W-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations
    • Arrar, M.; de Oliveira, C. A. F.; Fajer, M.; Sinko, W.; McCammon, J. A. w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations J. Chem. Theory Comput. 2013, 9 (1) 18-23
    • (2013) J. Chem. Theory Comput. , vol.9 , Issue.1 , pp. 18-23
    • Arrar, M.1    De Oliveira, C.A.F.2    Fajer, M.3    Sinko, W.4    McCammon, J.A.5
  • 19
    • 63449118443 scopus 로고    scopus 로고
    • Using Generalized Ensemble Simulations and Markov State Models to Identify Conformational States
    • Bowman, G. R.; Huang, X.; Pande, V. S. Using Generalized Ensemble Simulations and Markov State Models to Identify Conformational States Methods 2009, 49 (2) 197-201
    • (2009) Methods , vol.49 , Issue.2 , pp. 197-201
    • Bowman, G.R.1    Huang, X.2    Pande, V.S.3
  • 20
    • 0342929614 scopus 로고
    • Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
    • Torrie, G. M.; Valleau, J. P. Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling J. Comput. Phys. 1977, 23 (2) 187-199
    • (1977) J. Comput. Phys. , vol.23 , Issue.2 , pp. 187-199
    • Torrie, G.M.1    Valleau, J.P.2
  • 21
    • 84986519238 scopus 로고
    • The Weighted Histogram Analysis Method for Free-Energy Calculations on Biomolecules 0.1. The Method
    • Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. The Weighted Histogram Analysis Method for Free-Energy Calculations on Biomolecules 0.1. The Method J. Comput. Chem. 1992, 13 (8) 1011-1021
    • (1992) J. Comput. Chem. , vol.13 , Issue.8 , pp. 1011-1021
    • Kumar, S.1    Bouzida, D.2    Swendsen, R.H.3    Kollman, P.A.4    Rosenberg, J.M.5
  • 22
    • 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. L. Metadynamics: A Method to Simulate Rare Events and Reconstruct the Free Energy in Biophysics, Chemistry, and Material Science Rep. Prog. Phys. 2008, 71 (12) 126601
    • (2008) Rep. Prog. Phys. , vol.71 , Issue.12 , pp. 126601
    • Laio, A.1    Gervasio, F.L.2
  • 23
    • 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 (20) 9169-9183
    • (2001) J. Chem. Phys. , vol.115 , Issue.20 , pp. 9169-9183
    • Darve, E.1    Pohorille, A.2
  • 24
    • 42149194240 scopus 로고    scopus 로고
    • Adaptive Biasing Force Method for Scalar and Vector Free Energy Calculations
    • Darve, E.; Rodriguez-Gomez, D.; Pohorille, A. Adaptive Biasing Force Method for Scalar and Vector Free Energy Calculations J. Chem. Phys. 2008, 128 (14) 144120
    • (2008) J. Chem. Phys. , vol.128 , Issue.14 , pp. 144120
    • Darve, E.1    Rodriguez-Gomez, D.2    Pohorille, A.3
  • 25
    • 84863366516 scopus 로고    scopus 로고
    • Practically Efficient and Robust Free Energy Calculations: Double-Integration Orthogonal Space Tempering
    • Zheng, L. Q.; Yang, W. Practically Efficient and Robust Free Energy Calculations: Double-Integration Orthogonal Space Tempering J. Chem. Theory Comput. 2012, 8 (3) 810-823
    • (2012) J. Chem. Theory Comput. , vol.8 , Issue.3 , pp. 810-823
    • Zheng, L.Q.1    Yang, W.2
  • 26
    • 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. U.S.A. 2008, 105 (51) 20227-32
    • (2008) Proc. Natl. Acad. Sci. U.S.A. , vol.105 , Issue.51 , pp. 20227-20232
    • Zheng, L.1    Chen, M.2    Yang, W.3
  • 27
    • 4243754128 scopus 로고    scopus 로고
    • Nonequilibrium Equality for Free Energy Differences
    • Jarzynski, C. Nonequilibrium Equality for Free Energy Differences Phys. Rev. Lett. 1997, 78 (14) 2690-2693
    • (1997) Phys. Rev. Lett. , vol.78 , Issue.14 , pp. 2690-2693
    • Jarzynski, C.1
  • 28
    • 4244116139 scopus 로고    scopus 로고
    • Equilibrium Free-Energy Differences from Nonequilibrium Measurements: A Master-Equation Approach
    • Jarzynski, C. Equilibrium Free-Energy Differences from Nonequilibrium Measurements: A Master-Equation Approach Phys. Rev. E 1997, 56 (5) 5018-5035
    • (1997) Phys. Rev. e , vol.56 , Issue.5 , pp. 5018-5035
    • Jarzynski, C.1
  • 29
    • 0035333627 scopus 로고    scopus 로고
    • Fast-Growth Thermodynamic Integration: Error and Efficiency Analysis
    • Hummer, G. Fast-Growth Thermodynamic Integration: Error and Efficiency Analysis J. Chem. Phys. 2001, 114 (17) 7330-7337
    • (2001) J. Chem. Phys. , vol.114 , Issue.17 , pp. 7330-7337
    • Hummer, G.1
  • 30
    • 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 (6) 3559-3566
    • (2003) J. Chem. Phys. , vol.119 , Issue.6 , pp. 3559-3566
    • Park, S.1    Khalili-Araghi, F.2    Tajkhorshid, E.3    Schulten, K.4
  • 31
    • 5544264558 scopus 로고
    • Gaussian Fluctuation Formula for Electrostatic Free-Energy Changes in Solution
    • Levy, R. M.; Belhadj, M.; Kitchen, D. B. Gaussian Fluctuation Formula for Electrostatic Free-Energy Changes in Solution J. Chem. Phys. 1991, 95 (5) 3627-3633
    • (1991) J. Chem. Phys. , vol.95 , Issue.5 , pp. 3627-3633
    • Levy, R.M.1    Belhadj, M.2    Kitchen, D.B.3
  • 32
    • 0001085206 scopus 로고    scopus 로고
    • Classical and quantum simulations of tryptophan in solution
    • Simonson, T.; Wong, C. F.; Brunger, A. T. Classical and quantum simulations of tryptophan in solution J. Phys. Chem. A 1997, 101 (10) 1935-1945
    • (1997) J. Phys. Chem. A , vol.101 , Issue.10 , pp. 1935-1945
    • Simonson, T.1    Wong, C.F.2    Brunger, A.T.3
  • 34
    • 0036733958 scopus 로고    scopus 로고
    • Statistical Mechanical Refinement of Protein Structure Prediction Schemes: Cumulant Expansion Approach
    • Eastwood, M. P.; Hardin, C.; Luthey-Schulten, Z.; Wolynes, P. G. Statistical Mechanical Refinement of Protein Structure Prediction Schemes: Cumulant Expansion Approach J. Chem. Phys. 2002, 117 (9) 4602-4615
    • (2002) J. Chem. Phys. , vol.117 , Issue.9 , pp. 4602-4615
    • Eastwood, M.P.1    Hardin, C.2    Luthey-Schulten, Z.3    Wolynes, P.G.4
  • 35
    • 39749132831 scopus 로고    scopus 로고
    • Full Correlation Analysis of Conformational Protein Dynamics
    • Lange, O. F.; Grubmuller, H. Full Correlation Analysis of Conformational Protein Dynamics Proteins: Struct., Funct., Bioinf. 2008, 70 (4) 1294-1312
    • (2008) Proteins: Struct., Funct., Bioinf. , vol.70 , Issue.4 , pp. 1294-1312
    • Lange, O.F.1    Grubmuller, H.2
  • 37
    • 84860767348 scopus 로고    scopus 로고
    • Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born
    • Gotz, A. W.; Williamson, M. J.; Xu, D.; Poole, D.; Le Grand, S.; Walker, R. C. Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born J. Chem. Theory Comput. 2012, 8 (5) 1542-1555
    • (2012) J. Chem. Theory Comput. , vol.8 , Issue.5 , pp. 1542-1555
    • Gotz, A.W.1    Williamson, M.J.2    Xu, D.3    Poole, D.4    Le Grand, S.5    Walker, R.C.6
  • 38
    • 84884192184 scopus 로고    scopus 로고
    • Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald
    • Salomon-Ferrer, R.; Götz, A. W.; Poole, D.; Le Grand, S.; Walker, R. C. Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald J. Chem. Theory Comput. 2013, 9 (9) 3878-3888
    • (2013) J. Chem. Theory Comput. , vol.9 , Issue.9 , pp. 3878-3888
    • Salomon-Ferrer, R.1    Götz, A.W.2    Poole, D.3    Le Grand, S.4    Walker, R.C.5
  • 40
    • 84868214675 scopus 로고    scopus 로고
    • SPFP: Speed without Compromise - A Mixed Precision Model for GPU Accelerated Molecular Dynamics Simulations
    • Le Grand, S.; Gotz, A. W.; Walker, R. C. SPFP: Speed without Compromise - A Mixed Precision Model for GPU Accelerated Molecular Dynamics Simulations Comput. Phys. Commun. 2013, 184 (2) 374-380
    • (2013) Comput. Phys. Commun. , vol.184 , Issue.2 , pp. 374-380
    • Le Grand, S.1    Gotz, A.W.2    Walker, R.C.3
  • 43
    • 33646940952 scopus 로고
    • Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n -Alkanes
    • Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. C. Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n -Alkanes J. Comput. Phys. 1977, 23 (3) 327-341
    • (1977) J. Comput. Phys. , vol.23 , Issue.3 , pp. 327-341
    • Ryckaert, J.-P.1    Ciccotti, G.2    Berendsen, H.J.C.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.