-
1
-
-
84962477148
-
Structure/Function Correlations of Proteins Using MM, QM/MM, and Related Approaches: Methods, Concepts, Pitfalls, and Current Progress
-
Shurki, A.; Warshel, A. Structure/Function Correlations of Proteins Using MM, QM/MM, and Related Approaches: Methods, Concepts, Pitfalls, and Current Progress Adv. Protein Chem. 2003, 66, 249-313
-
(2003)
Adv. Protein Chem.
, vol.66
, pp. 249-313
-
-
Shurki, A.1
Warshel, A.2
-
2
-
-
60349127442
-
QM/MM Methods for Biomolecular Systems
-
Senn, H. M.; Thiel, W. QM/MM Methods for Biomolecular Systems Angew. Chem., Int. Ed. 2009, 48, 1198-1229
-
(2009)
Angew. Chem., Int. Ed.
, vol.48
, pp. 1198-1229
-
-
Senn, H.M.1
Thiel, W.2
-
3
-
-
0036025446
-
Quantum Mechanical Methods for Enzyme Kinetics
-
Gao, J. L.; Truhlar, D. G. Quantum Mechanical Methods for Enzyme Kinetics Annu. Rev. Phys. Chem. 2002, 53, 467-505
-
(2002)
Annu. Rev. Phys. Chem.
, vol.53
, pp. 467-505
-
-
Gao, J.L.1
Truhlar, D.G.2
-
4
-
-
21244497608
-
Ab Initio Quantum Chemical and Mixed Quantum Mechanics/Molecular Mechanics (QM/MM) Methods for Studying Enzymatic Catalysis
-
Friesner, R. A.; Guallar, V. Ab Initio Quantum Chemical and Mixed Quantum Mechanics/Molecular Mechanics (QM/MM) Methods for Studying Enzymatic Catalysis Annu. Rev. Phys. Chem. 2005, 56, 389-427
-
(2005)
Annu. Rev. Phys. Chem.
, vol.56
, pp. 389-427
-
-
Friesner, R.A.1
Guallar, V.2
-
5
-
-
43949083733
-
Free Energies of Chemical Reactions in Solution and in Enzymes with Ab Initio Quantum Mechanics/Molecular Mechanics Methods
-
Hu, H.; Yang, W. T. Free Energies of Chemical Reactions in Solution and in Enzymes with Ab Initio Quantum Mechanics/Molecular Mechanics Methods Annu. Rev. Phys. Chem. 2008, 59, 573-601
-
(2008)
Annu. Rev. Phys. Chem.
, vol.59
, pp. 573-601
-
-
Hu, H.1
Yang, W.T.2
-
6
-
-
33646356998
-
Development of Effective Quantum Mechanical/Molecular Mechanical (QM/MM) Methods for Complex Biological Processes
-
Riccardi, D.; Schaefer, P.; Yang, Y.; Yu, H. B.; Ghosh, N.; Prat-Resina, X.; Konig, P.; Li, G. H.; Xu, D. G.; Guo, H.; Elstner, M.; Cui, Q. Development of Effective Quantum Mechanical/Molecular Mechanical (QM/MM) Methods for Complex Biological Processes J. Phys. Chem. B 2006, 110, 6458-6469
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 6458-6469
-
-
Riccardi, D.1
Schaefer, P.2
Yang, Y.3
Yu, H.B.4
Ghosh, N.5
Prat-Resina, X.6
Konig, P.7
Li, G.H.8
Xu, D.G.9
Guo, H.10
Elstner, M.11
Cui, Q.12
-
8
-
-
33748263629
-
Pseudobond Ab Initio QM/MM Approach and Its Applications to Enzyme Reactions
-
Zhang, Y. Pseudobond Ab Initio QM/MM Approach and Its Applications to Enzyme Reactions Theor. Chem. Acc. 2006, 116, 43-50
-
(2006)
Theor. Chem. Acc.
, vol.116
, pp. 43-50
-
-
Zhang, Y.1
-
9
-
-
33646940952
-
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, 327-341
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
10
-
-
84986440341
-
Settle - An Analytical Version of the Shake and Rattle Algorithm for Rigid Water Models
-
Miyamoto, S.; Kollman, P. A. Settle-An Analytical Version of the Shake and Rattle Algorithm for Rigid Water Models J. Comput. Chem. 1992, 13, 952-962
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 952-962
-
-
Miyamoto, S.1
Kollman, P.A.2
-
11
-
-
0000388705
-
Lincs: A Linear Constraint Solver for Molecular Simulations
-
Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. Lincs: A Linear Constraint Solver for Molecular Simulations J. Comput. Chem. 1997, 18, 1463-1472
-
(1997)
J. Comput. Chem.
, vol.18
, pp. 1463-1472
-
-
Hess, B.1
Bekker, H.2
Berendsen, H.J.C.3
Fraaije, J.4
-
12
-
-
0000525633
-
Effect of Constraints on the Dynamics of Macromolecules
-
Van Gunsteren, W. F.; Karplus, M. Effect of Constraints on the Dynamics of Macromolecules Macromolecules 1982, 15, 1528-1544
-
(1982)
Macromolecules
, vol.15
, pp. 1528-1544
-
-
Van Gunsteren, W.F.1
Karplus, M.2
-
14
-
-
0345491105
-
Development of the Colle-Salvetti Correlation Energy Formula into a Functional of the Electron Density
-
Lee, C.; Yang, W. T.; Parr, R. G. Development of the Colle-Salvetti Correlation Energy Formula into a Functional of the Electron Density Phys. Rev. B 1988, 37, 785-789
-
(1988)
Phys. Rev. B
, vol.37
, pp. 785-789
-
-
Lee, C.1
Yang, W.T.2
Parr, R.G.3
-
15
-
-
0000189651
-
Density-Functional Thermochemistry. III. The Role of Exact Exchange
-
Becke, A. D. Density-Functional Thermochemistry. III. The Role of Exact Exchange J. Chem. Phys. 1993, 98, 5648-5652
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 5648-5652
-
-
Becke, A.D.1
-
16
-
-
0004016501
-
Comparison of Simple Potential Functions for Simulating Liquid Water
-
Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of Simple Potential Functions for Simulating Liquid Water J. Chem. Phys. 1983, 79, 926-935
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
17
-
-
33750587438
-
Molecular Dynamics with Coupling to an External Bath
-
Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. Molecular Dynamics with Coupling to an External Bath J. Chem. Phys. 1984, 81, 3684-3690
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Dinola, A.4
Haak, J.R.5
-
18
-
-
0000733745
-
-
In; Schleyer, P. v. R. Wiley: New York, Vol.
-
Jorgensen, W. L. In Encyclopedia of Computational Chemistry; Schleyer, P. v. R., Ed.; Wiley: New York, 1998; Vol. 3, p 1986-1989.
-
(1998)
Encyclopedia of Computational Chemistry
, vol.3
, pp. 1986-1989
-
-
Jorgensen, W.L.1
-
19
-
-
46249092554
-
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
-
-
34547809547
-
Unified Formulation of the Constant Temperature Molecular-Dynamics Methods
-
Nose, S. A Unified Formulation of the Constant Temperature Molecular-Dynamics Methods J. Chem. Phys. 1984, 81, 511-519
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 511-519
-
-
Nose, S.A.1
-
21
-
-
0001538909
-
Canonical Dynamics - Equilibrium Phase-Space Distributions
-
Hoover, W. G. Canonical Dynamics-Equilibrium Phase-Space Distributions Phys. Rev. A 1985, 31, 1695-1697
-
(1985)
Phys. Rev. A
, vol.31
, pp. 1695-1697
-
-
Hoover, W.G.1
-
22
-
-
33846086933
-
Canonical Sampling through Velocity Rescaling
-
Bussi, G.; Donadio, D.; Parrinello, M. Canonical Sampling through Velocity Rescaling J. Chem. Phys. 2007, 126, 014101
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 014101
-
-
Bussi, G.1
Donadio, D.2
Parrinello, M.3
-
24
-
-
33846823909
-
Particle Mesh Ewald: An N.Log(N) Method for Ewald Sums in Large Systems
-
Darden, T. A.; York, D. M.; Pedersen, L. G. 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
-
25
-
-
33645961739
-
A Smooth Particle Mesh Ewald Method
-
Essmann, U.; Perera, L.; Berkowitz, M.; Darden, T.; Lee, H.; Pedersen, L. A Smooth Particle Mesh Ewald Method J. Chem. Phys. 1995, 103, 8577-8593
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.3
Darden, T.4
Lee, H.5
Pedersen, L.6
-
26
-
-
0034702646
-
Fluctuation Formulas in Molecular-Dynamics Simulations with the Weak Coupling Heat Bath
-
Morishita, T. Fluctuation Formulas in Molecular-Dynamics Simulations with the Weak Coupling Heat Bath J. Chem. Phys. 2000, 113, 2976-2982
-
(2000)
J. Chem. Phys.
, vol.113
, pp. 2976-2982
-
-
Morishita, T.1
-
27
-
-
0009987595
-
Simulations of Vibrational Relaxation in Dense Molecular Fluids. I. Methods
-
Holian, B. L. Simulations of Vibrational Relaxation in Dense Molecular Fluids. I. Methods J. Chem. Phys. 1986, 84, 3138-3146
-
(1986)
J. Chem. Phys.
, vol.84
, pp. 3138-3146
-
-
Holian, B.L.1
-
28
-
-
46149089973
-
Simulations of Proteins with Inhomogeneous Degrees of Freedom: The Effect of Thermostats
-
Mor, A.; Ziv, G.; Levy, Y. Simulations of Proteins with Inhomogeneous Degrees of Freedom: The Effect of Thermostats J. Comput. Chem. 2008, 29, 1992-1998
-
(2008)
J. Comput. Chem.
, vol.29
, pp. 1992-1998
-
-
Mor, A.1
Ziv, G.2
Levy, Y.3
-
29
-
-
79251622248
-
Equipartition and the Calculation of Temperature in Biomolecular Simulations
-
Eastwood, M. P.; Stafford, K. A.; Lippert, R. A.; Jensen, M. O.; Maragakis, P.; Predescu, C.; Dror, R. O.; Shaw, D. E. Equipartition and the Calculation of Temperature in Biomolecular Simulations J. Chem. Theory Comput. 2010, 6, 2045-2058
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 2045-2058
-
-
Eastwood, M.P.1
Stafford, K.A.2
Lippert, R.A.3
Jensen, M.O.4
Maragakis, P.5
Predescu, C.6
Dror, R.O.7
Shaw, D.E.8
-
31
-
-
26044480933
-
Mass Tensor Molecular-Dynamics
-
Bennett, C. H. Mass Tensor Molecular-Dynamics J. Comput. Phys. 1975, 19, 267-279
-
(1975)
J. Comput. Phys.
, vol.19
, pp. 267-279
-
-
Bennett, C.H.1
-
32
-
-
0000334103
-
-
In; Franks, F. Plenum Press: New York, Vol.
-
Wood, D. W. In Water: A Comprehensive Treatise; Franks, F., Ed.; Plenum Press: New York, 1979; Vol. 6, p 279.
-
(1979)
Water: A Comprehensive Treatise
, vol.6
, pp. 279
-
-
Wood, D.W.1
-
33
-
-
70349895348
-
Increasing the Time Step with Mass Scaling in Born-Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations
-
Zheng, H.; Wang, S.; Zhang, Y. Increasing the Time Step with Mass Scaling in Born-Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations J. Comput. Chem. 2009, 30, 2706-2711
-
(2009)
J. Comput. Chem.
, vol.30
, pp. 2706-2711
-
-
Zheng, H.1
Wang, S.2
Zhang, Y.3
-
34
-
-
0001585978
-
Improving Efficiency of Large Time-Scale Molecular Dynamics Simulations of Hydrogen-Rich Systems
-
Feenstra, K. A.; Hess, B.; Berendsen, H. J. C. Improving Efficiency of Large Time-Scale Molecular Dynamics Simulations of Hydrogen-Rich Systems J. Comput. Chem. 1999, 20, 786-798
-
(1999)
J. Comput. Chem.
, vol.20
, pp. 786-798
-
-
Feenstra, K.A.1
Hess, B.2
Berendsen, H.J.C.3
-
35
-
-
0037180863
-
Ab Initio QM/MM Simulation with Proper Sampling: ″first Principle″ Calculations of the Free Energy of the Autodissociation of Water in Aqueous Solution
-
Strajbl, M.; Hong, G.; Warshel, A. Ab Initio QM/MM Simulation with Proper Sampling: ″First Principle″ Calculations of the Free Energy of the Autodissociation of Water in Aqueous Solution J. Phys. Chem. B 2002, 106, 13333-13343
-
(2002)
J. Phys. Chem. B
, vol.106
, pp. 13333-13343
-
-
Strajbl, M.1
Hong, G.2
Warshel, A.3
-
36
-
-
79959339177
-
Paradynamics: An Effective and Reliable Model for Ab Lnitio QM/MM Free-Energy Calculations and Related Tasks
-
Plotnikov, N. V.; Kamerlin, S. C. L.; Warshel, A. Paradynamics: An Effective and Reliable Model for Ab Lnitio QM/MM Free-Energy Calculations and Related Tasks J. Phys. Chem. B 2011, 115, 7950-7962
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 7950-7962
-
-
Plotnikov, N.V.1
Kamerlin, S.C.L.2
Warshel, A.3
-
37
-
-
2942538198
-
Chaperoned Alchemical Free Energy Simulations: A General Method for QM, MM, and QM/MM Potentials
-
Yang, W.; Bitetti-Putzer, R.; Karplus, M. Chaperoned Alchemical Free Energy Simulations: A General Method for QM, MM, and QM/MM Potentials J. Chem. Phys. 2004, 120, 9450-9453
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 9450-9453
-
-
Yang, W.1
Bitetti-Putzer, R.2
Karplus, M.3
-
38
-
-
38349143673
-
Quantum Mechanics/Molecular Mechanics Minimum Free-Energy Path for Accurate Reaction Energetics in Solution and Enzymes: Sequential Sampling and Optimization on the Potential of Mean Force Surface
-
Hu, H.; Lu, Z. Y.; Parks, J. M.; Burger, S. K.; Yang, W. T. Quantum Mechanics/Molecular Mechanics Minimum Free-Energy Path for Accurate Reaction Energetics in Solution and Enzymes: Sequential Sampling and Optimization on the Potential of Mean Force Surface J. Chem. Phys. 2008, 128, 034105
-
(2008)
J. Chem. Phys.
, vol.128
, pp. 034105
-
-
Hu, H.1
Lu, Z.Y.2
Parks, J.M.3
Burger, S.K.4
Yang, W.T.5
-
39
-
-
34248224411
-
QM/MM Minimum Free-Energy Path: Methodology and Application to Triosephosphate Isomerase
-
Hu, H.; Lu, Z. Y.; Yang, W. T. QM/MM Minimum Free-Energy Path: Methodology and Application to Triosephosphate Isomerase J. Chem. Theory Comput. 2007, 3, 390-406
-
(2007)
J. Chem. Theory Comput.
, vol.3
, pp. 390-406
-
-
Hu, H.1
Lu, Z.Y.2
Yang, W.T.3
-
40
-
-
0000145441
-
Free Energy Calculation on Enzyme Reactions with an Efficient Iterative Procedure to Determine Minimum Energy Paths on a Combined Ab Initio QM/MM Potential Energy Surface
-
Zhang, Y.; Liu, H.; Yang, W. T. Free Energy Calculation on Enzyme Reactions with an Efficient Iterative Procedure to Determine Minimum Energy Paths on a Combined Ab Initio QM/MM Potential Energy Surface J. Chem. Phys. 2000, 112, 3483-3492
-
(2000)
J. Chem. Phys.
, vol.112
, pp. 3483-3492
-
-
Zhang, Y.1
Liu, H.2
Yang, W.T.3
-
41
-
-
84876717781
-
QM/MM Simulations of Vibrational Spectra of Bacteriorhodopsin and Channelrhodopsin-2
-
Welke, K.; Watanabe, H. C.; Wolter, T.; Gaus, M.; Elstner, M. QM/MM Simulations of Vibrational Spectra of Bacteriorhodopsin and Channelrhodopsin-2 Phys. Chem. Chem. Phys. 2013, 15, 6651-6659
-
(2013)
Phys. Chem. Chem. Phys.
, vol.15
, pp. 6651-6659
-
-
Welke, K.1
Watanabe, H.C.2
Wolter, T.3
Gaus, M.4
Elstner, M.5
-
42
-
-
84867647953
-
Vibrational Spectra of Water Solutions of Azoles from QM/MM Calculations: Effects of Solvation
-
Tanzi, L.; Ramondo, F.; Guidoni, L. Vibrational Spectra of Water Solutions of Azoles from QM/MM Calculations: Effects of Solvation J. Phys. Chem. A 2012, 116, 10160-10171
-
(2012)
J. Phys. Chem. A
, vol.116
, pp. 10160-10171
-
-
Tanzi, L.1
Ramondo, F.2
Guidoni, L.3
-
43
-
-
85067740362
-
Vibrational Spectroscopy of Biomolecules by Mixed Quantum/Classical Molecular Dynamics
-
Bovi, D.; Spezia, R.; Mezzetti, A.; Vuilleumier, R.; Gaigeot, M.-P.; Guidoni, L. Vibrational Spectroscopy of Biomolecules by Mixed Quantum/Classical Molecular Dynamics Eur. Biophys. J. 2011, 40, 102-102
-
(2011)
Eur. Biophys. J.
, vol.40
, pp. 102-102
-
-
Bovi, D.1
Spezia, R.2
Mezzetti, A.3
Vuilleumier, R.4
Gaigeot, M.-P.5
Guidoni, L.6
-
44
-
-
42149100111
-
The Implementation of a Fast and Accurate QM/MM Potential Method in Amber
-
Walker, R. C.; Crowley, M. F.; Case, D. A. The Implementation of a Fast and Accurate QM/MM Potential Method in Amber J. Comput. Chem. 2008, 29, 1019-1031
-
(2008)
J. Comput. Chem.
, vol.29
, pp. 1019-1031
-
-
Walker, R.C.1
Crowley, M.F.2
Case, D.A.3
-
45
-
-
0242395926
-
The Nature of K+ Crown-Ether Interactions - A Hybrid Quantum Mechanical-Molecular Mechanical Study
-
Thompson, M. A.; Glendening, E. D.; Feller, D. The Nature of K+ Crown-Ether Interactions-a Hybrid Quantum Mechanical-Molecular Mechanical Study J. Phys. Chem. 1994, 98, 10465-10476
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 10465-10476
-
-
Thompson, M.A.1
Glendening, E.D.2
Feller, D.3
-
46
-
-
83455203339
-
QM/MM Simulation of Liquid Water with an Adaptive Quantum Region
-
Bernstein, N.; Varnai, C.; Solt, I.; Winfield, S. A.; Payne, M. C.; Simon, I.; Fuxreiter, M.; Csanyi, G. QM/MM Simulation of Liquid Water with an Adaptive Quantum Region Phys. Chem. Chem. Phys. 2012, 14, 646-656
-
(2012)
Phys. Chem. Chem. Phys.
, vol.14
, pp. 646-656
-
-
Bernstein, N.1
Varnai, C.2
Solt, I.3
Winfield, S.A.4
Payne, M.C.5
Simon, I.6
Fuxreiter, M.7
Csanyi, G.8
-
47
-
-
0031208134
-
Solvation of Ca2+ in Water Studied by Born-Oppenheimer Ab Initio QM/MM Dynamics
-
Tongraar, A.; Liedl, K. R.; Rode, B. M. Solvation of Ca2+ in Water Studied by Born-Oppenheimer Ab Initio QM/MM Dynamics J. Phys. Chem. A 1997, 101, 6299-6309
-
(1997)
J. Phys. Chem. A
, vol.101
, pp. 6299-6309
-
-
Tongraar, A.1
Liedl, K.R.2
Rode, B.M.3
-
48
-
-
0017251977
-
Bicycle-Pedal Model for 1st Step in Vision Process
-
Warshel, A. Bicycle-Pedal Model for 1st Step in Vision Process Nature 1976, 260, 679-683
-
(1976)
Nature
, vol.260
, pp. 679-683
-
-
Warshel, A.1
|