-
1
-
-
34548717559
-
Phase transition for a hard sphere system
-
Alder BJ, Wainwright TE. Phase transition for a hard sphere system. J Chem Phys. 1957; 27: 1208-1209.
-
(1957)
J Chem Phys
, vol.27
, pp. 1208-1209
-
-
Alder, B.J.1
Wainwright, T.E.2
-
3
-
-
84878381053
-
Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics
-
Zhao G, Perilla JR, Yufenyuy EL, Meng X, Chen B, Ning J, Ahn J, Gronenborn AM, Schulten K, Aiken C, Zhang P. Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Nature. 2013; 497: 643-646.
-
(2013)
Nature
, vol.497
, pp. 643-646
-
-
Zhao, G.1
Perilla, J.R.2
Yufenyuy, E.L.3
Meng, X.4
Chen, B.5
Ning, J.6
Ahn, J.7
Gronenborn, A.M.8
Schulten, K.9
Aiken, C.10
Zhang, P.11
-
4
-
-
35348886062
-
Anton, a special-purpose machine for molecular dynamics simulation, SIGARCH Comput
-
Shaw DE, Deneroff MM, Dror RO, Kuskin JS, Larson RH, Salmon JK, Young C, Batson B, Bowers KJ, Chao JC, Eastwood MP, Gagliardo J, Grossman JP, Ho CR, Ierardi DJ, Kolossváry I, Klepeis JL, Layman T, McLeavey C, Moraes MA, Mueller R, Priest EC, Shan Y, Spengler J, Theobald M, Towles B, Wang SC. Anton, a special-purpose machine for molecular dynamics simulation, SIGARCH Comput. Archit News. 2007; 35: 1-12.
-
(2007)
Archit News
, vol.35
, pp. 1-12
-
-
Shaw, D.E.1
Deneroff, M.M.2
Dror, R.O.3
Kuskin, J.S.4
Larson, R.H.5
Salmon, J.K.6
Young, C.7
Batson, B.8
Bowers, K.J.9
Chao, J.C.10
Eastwood, M.P.11
Gagliardo, J.12
Grossman, J.P.13
Ho, C.R.14
Ierardi, D.J.15
Kolossváry, I.16
Klepeis, J.L.17
Layman, T.18
McLeavey, C.19
Moraes, M.A.20
Mueller, R.21
Priest, E.C.22
Shan, Y.23
Spengler, J.24
Theobald, M.25
Towles, B.26
Wang, S.C.27
more..
-
7
-
-
0001616080
-
Replica-exchange molecular dynamics method for protein folding
-
Sugita Y, Okamoto Y. Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett. 1999; 314: 141-151.
-
(1999)
Chem Phys Lett
, vol.314
, pp. 141-151
-
-
Sugita, Y.1
Okamoto, Y.2
-
8
-
-
0034294024
-
Multidimensional replica-exchange method for free-energy calculations
-
Sugita Y, Kitao A, Okamoto Y. Multidimensional replica-exchange method for free-energy calculations. J Chem Phys. 2000; 113: 6042-6051.
-
(2000)
J Chem Phys
, vol.113
, pp. 6042-6051
-
-
Sugita, Y.1
Kitao, A.2
Okamoto, Y.3
-
9
-
-
36849102835
-
Monte Carlo estimation of the free energy by multistage sampling
-
Valleau JP, Card DN. Monte Carlo estimation of the free energy by multistage sampling. J Chem Phys. 1972; 57: 5457-5462.
-
(1972)
J Chem Phys
, vol.57
, pp. 5457-5462
-
-
Valleau, J.P.1
Card, D.N.2
-
10
-
-
36749113356
-
Monte Carlo study of phase separating liquid mixture by umbrella sampling
-
Torrie GM, Valleau JP. Monte Carlo study of phase separating liquid mixture by umbrella sampling. J Chem Phys. 1977; 66: 1402-1408.
-
(1977)
J Chem Phys
, vol.66
, pp. 1402-1408
-
-
Torrie, G.M.1
Valleau, J.P.2
-
11
-
-
0028710015
-
Local elevation: A method for improving the searching properties of molecular dynamics simulation
-
Huber T, Torda AE, van Gunsteren WF. 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.E.2
Van Gunsteren, W.F.3
-
12
-
-
0000689085
-
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
-
13
-
-
0035935802
-
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
-
14
-
-
84896743415
-
Frontiers in free-energy calculations of biological systems
-
Chipot C. Frontiers in free-energy calculations of biological systems. Wiley Interdiscip Rev Comput Mol Sci. 2013.
-
(2013)
Wiley Interdiscip Rev Comput Mol Sci
-
-
Chipot, C.1
-
15
-
-
77951140202
-
Potential of mean force calculations: A multiple-walker adaptive biasing force approach
-
Minoukadeh K, Chipot C, Lelièvre T. Potential of mean force calculations: a multiple-walker adaptive biasing force approach. J Chem Theory Comput. 2010; 6: 1008-1017.
-
(2010)
J Chem Theory Comput
, vol.6
, pp. 1008-1017
-
-
Minoukadeh, K.1
Chipot, C.2
Lelièvre, T.3
-
16
-
-
4344660645
-
Overcoming free energy barriers using unconstrained molecular dynamics simulations
-
Hénin J, Chipot C. Overcoming free energy barriers using unconstrained molecular dynamics simulations. J Chem Phys. 2004; 121: 2904-2914.
-
(2004)
J Chem Phys
, vol.121
, pp. 2904-2914
-
-
Hénin, J.1
Chipot, C.2
-
18
-
-
36849122972
-
High-temperature equation of state by a perturbation method. I. Nonpolar gases
-
Zwanzig RW. High-temperature equation of state by a perturbation method. I. Nonpolar gases. J Chem Phys. 1954; 22: 1420-1426.
-
(1954)
J Chem Phys
, vol.22
, pp. 1420-1426
-
-
Zwanzig, R.W.1
-
19
-
-
4243661501
-
Constrained reaction coordinate dynamics for the simulation of rare events
-
Carter E, 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.1
Ciccotti, G.2
Hynes, J.T.3
Kapral, R.4
-
20
-
-
58149512801
-
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 USA. 2008; 105: 20227-20232.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 20227-20232
-
-
Zheng, L.1
Chen, M.2
Yang, W.3
-
21
-
-
77955577540
-
Good practices in free-energy calculations
-
Pohorille A, Jarzynski C, Chipot C. Good practices in free-energy calculations. J Phys Chem B. 2010; 114: 10235-10253.
-
(2010)
J Phys Chem B
, vol.114
, pp. 10235-10253
-
-
Pohorille, A.1
Jarzynski, C.2
Chipot, C.3
-
22
-
-
33646471468
-
Statistical mechanics of fluid mixtures
-
Kirkwood JG. Statistical mechanics of fluid mixtures. J Chem Phys. 1935; 3: 300-313.
-
(1935)
J Chem Phys
, vol.3
, pp. 300-313
-
-
Kirkwood, J.G.1
-
23
-
-
0346350789
-
The development of replica-exchange-based free-energy methods
-
Woods CJ, Essex JW, King MA. The development of replica-exchange-based free-energy methods. J Phys Chem B. 2003; 107: 13703-13710.
-
(2003)
J Phys Chem B
, vol.107
, pp. 13703-13710
-
-
Woods, C.J.1
Essex, J.W.2
King, M.A.3
-
24
-
-
73949121918
-
Computation of absolute hydration and binding free energy with free energy perturbation distributed replica-exchange molecular dynamics
-
Jiang W, Hodoscek M, Roux B. Computation of absolute hydration and binding free energy with free energy perturbation distributed replica-exchange molecular dynamics. J Chem Theory Comput. 2009; 5: 2583-2588.
-
(2009)
J Chem Theory Comput
, vol.5
, pp. 2583-2588
-
-
Jiang, W.1
Hodoscek, M.2
Roux, B.3
-
25
-
-
77956574437
-
Free energy perturbation Hamiltonian replica-exchange molecular dynamics (FEP/H-REMD) for absolute ligand binding free energy calculations
-
Jiang W, Roux B. Free energy perturbation Hamiltonian replica-exchange molecular dynamics (FEP/H-REMD) for absolute ligand binding free energy calculations. J Chem Theory Comput. 2010; 6: 2559-2565.
-
(2010)
J Chem Theory Comput
, vol.6
, pp. 2559-2565
-
-
Jiang, W.1
Roux, B.2
-
26
-
-
0031553195
-
Thermodynamic decomposition of hydration free energies by computer simulation: Application to amines, oxides, and sulfides
-
Kubo MM, Gallicchio E, Levy RM. Thermodynamic decomposition of hydration free energies by computer simulation: application to amines, oxides, and sulfides. J Phys Chem B. 1997; 101: 10527-10534.
-
(1997)
J Phys Chem B
, vol.101
, pp. 10527-10534
-
-
Kubo, M.M.1
Gallicchio, E.2
Levy, R.M.3
-
27
-
-
0032233055
-
Computer simulations with explicit solvent: Recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects
-
Levy RM, Gallicchio E. Computer simulations with explicit solvent: Recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects. Annu Rev Phys Chem. 1998; 49: 531-567.
-
(1998)
Annu Rev Phys Chem
, vol.49
, pp. 531-567
-
-
Levy, R.M.1
Gallicchio, E.2
-
28
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel L, Kalé RD, Schulten K. Scalable molecular dynamics with NAMD. J Comput Chem. 2005; 26: 1781-1802.
-
(2005)
J Comput Chem
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, L.8
Kalé, R.D.9
Schulten, K.10
-
29
-
-
0000695782
-
Understanding modern molecular dynamics: Techniques and applications
-
Tuckerman ME, Martyna GJ. Understanding modern molecular dynamics: Techniques and applications. J Phys Chem B. 2000; 104: 159-178.
-
(2000)
J Phys Chem B
, vol.104
, pp. 159-178
-
-
Tuckerman, M.E.1
Martyna, G.J.2
-
30
-
-
84986440341
-
Settle: An analytical version of the shake and rattle algorithms for rigid water models
-
Miyamoto S, Kollman PA. Settle: an analytical version of the shake and rattle algorithms 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
-
31
-
-
48749148224
-
Rattle: A velocity version of the shake algorithm for molecular dynamics calculations
-
Andersen HC. Rattle: a velocity version of the shake algorithm for molecular dynamics calculations. J Comput Phys. 1983; 52: 24-34.
-
(1983)
J Comput Phys
, vol.52
, pp. 24-34
-
-
Andersen, H.C.1
-
32
-
-
0042885340
-
Free energy calculation from steered molecular dynamics simulations using Jarzynskis equality
-
Park S, Khalili-Araghi F, Tajkhorshid E, Schulten K. Free energy calculation from steered molecular dynamics simulations using Jarzynskis equality. J Chem Phys. 2003; 119: 3559-3566.
-
(2003)
J Chem Phys
, vol.119
, pp. 3559-3566
-
-
Park, S.1
Khalili-Araghi, F.2
Tajkhorshid, E.3
Schulten, K.4
-
33
-
-
29744459271
-
Exploring the free energy landscape of a short peptide using an average force
-
Chipot C, Hénin J. Exploring the free energy landscape of a short peptide using an average force. J Chem Phys. 2005; 123: 244906.
-
(2005)
J Chem Phys
, vol.123
, pp. 244906
-
-
Chipot, C.1
Hénin, J.2
-
34
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell AD Jr., Bashford D, Bellott M, Dunbrack RL Jr., Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE III, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiórkiewicz-Kuczera J, Yin D, Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B. 1998; 102: 3586-3616.
-
(1998)
J Phys Chem B
, vol.102
, pp. 3586-3616
-
-
Mackerell Jr., A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack Jr., R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-Mccarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Roux, B.20
Schlenkrich, M.21
Smith, J.C.22
Stote, R.23
Straub, J.24
Watanabe, M.25
Wiórkiewicz- Kuczera, J.26
Yin, D.27
Karplus, M.28
more..
-
35
-
-
1642576012
-
Improved treatment of the protein backbone in empirical force fields
-
MacKerell AD, Feig M, Brooks CL. Improved treatment of the protein backbone in empirical force fields. J Am Chem Soc. 2004; 126: 698-699.
-
(2004)
J Am Chem Soc
, vol.126
, pp. 698-699
-
-
Mackerell, A.D.1
Feig, M.2
Brooks, C.L.3
-
36
-
-
76249087938
-
CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields
-
Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, Darian E, Guvench O, Lopes P, Vorobyov I, Mackerell AD Jr. CHARMM general force field: a force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J Comput Chem. 2010; 31: 671-690.
-
(2010)
J Comput Chem
, vol.31
, pp. 671-690
-
-
Vanommeslaeghe, K.1
Hatcher, E.2
Acharya, C.3
Kundu, S.4
Zhong, S.5
Shim, J.6
Darian, E.7
Guvench, O.8
Lopes, P.9
Vorobyov, I.10
Mackerell Jr., A.D.11
-
37
-
-
33846823909
-
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
-
38
-
-
34547314279
-
Characterization of conformational equilibria through Hamiltonian and temperature replica-exchange simulations: Assessing entropic and environmental effects
-
Faraldo-Gómez JD, Roux B. Characterization of conformational equilibria through Hamiltonian and temperature replica-exchange simulations: Assessing entropic and environmental effects. J Comput Chem. 2007; 28: 1634-1647.
-
(2007)
J Comput Chem
, vol.28
, pp. 1634-1647
-
-
Faraldo-Gómez, J.D.1
Roux, B.2
-
39
-
-
36449007836
-
Constant pressure molecular dynamics simulations-the Langevin piston method
-
Feller SE, Zhang YH, Pastor RW, Brooks BR. Constant pressure molecular dynamics simulations-the Langevin piston method. J Chem Phys. 1995; 103: 4613-4621.
-
(1995)
J Chem Phys
, vol.103
, pp. 4613-4621
-
-
Feller, S.E.1
Zhang, Y.H.2
Pastor, R.W.3
Brooks, B.R.4
-
40
-
-
77950102787
-
Exploring multidimensional free energy landscapes using time-dependent biases on collective variables
-
Hénin J, Fiorin G, Chipot C, Klein ML. Exploring multidimensional free energy landscapes using time-dependent biases on collective variables. J Chem Theory Comput. 2010; 6: 35-47.
-
(2010)
J Chem Theory Comput
, vol.6
, pp. 35-47
-
-
Hénin, J.1
Fiorin, G.2
Chipot, C.3
Klein, M.L.4
-
42
-
-
33645903407
-
Solvation thermodynamics of nonionic solutes
-
Ben-Naim A, Marcus Y. Solvation thermodynamics of nonionic solutes. J Chem Phys. 1984; 81: 2016-2027.
-
(1984)
J Chem Phys
, vol.81
, pp. 2016-2027
-
-
Ben-Naim, A.1
Marcus, Y.2
-
43
-
-
84865069022
-
A toolkit for the analysis of free-energy perturbation calculations
-
Liu P, Dehez F, Cai W, Chipot C. A toolkit for the analysis of free-energy perturbation calculations. J Chem Theory Comput. 2012; 8: 2606-2616.
-
(2012)
J Chem Theory Comput
, vol.8
, pp. 2606-2616
-
-
Liu, P.1
Dehez, F.2
Cai, W.3
Chipot, C.4
-
44
-
-
10844229225
-
Calculation of the aqueous solvation energy and entropy, as well as free energy, of simple polar solutes
-
Wan S, Stote RH, Karplus M. Calculation of the aqueous solvation energy and entropy, as well as free energy, of simple polar solutes. J Chem Phys. 2004; 121: 9539-9548.
-
(2004)
J Chem Phys
, vol.121
, pp. 9539-9548
-
-
Wan, S.1
Stote, R.H.2
Karplus, M.3
-
45
-
-
5244304444
-
Efficient estimation of free energy differences from Monte Carlo data
-
Bennett CH. Efficient estimation of free energy differences from Monte Carlo data. J Comput Phys. 1976; 22: 245-268.
-
(1976)
J Comput Phys
, vol.22
, pp. 245-268
-
-
Bennett, C.H.1
-
46
-
-
52949088587
-
Statistically optimal analysis of samples from multiple equilibrium states
-
Shirts MR, Chodera JD. Statistically optimal analysis of samples from multiple equilibrium states. J Chem Phys. 2008; 129: 124105.
-
(2008)
J Chem Phys
, vol.129
, pp. 124105
-
-
Shirts, M.R.1
Chodera, J.D.2
-
47
-
-
20444499328
-
Insights into the recognition and association of transmembrane α-helices. The free energy of α-helix dimerization in glycophorin A
-
Hénin J, Pohorille A, Chipot C. Insights into the recognition and association of transmembrane α-helices. The free energy of α-helix dimerization in glycophorin A. J Am Chem Soc. 2005; 127: 8478-8484.
-
(2005)
J Am Chem Soc
, vol.127
, pp. 8478-8484
-
-
Hénin, J.1
Pohorille, A.2
Chipot, C.3
|