-
1
-
-
0036725277
-
Molecular dynamics simulations of biomolecules
-
Karplus M., and McCammon J.A. Molecular dynamics simulations of biomolecules. Nat. Struct. Biol. 9 (2002) 646-652
-
(2002)
Nat. Struct. Biol.
, vol.9
, pp. 646-652
-
-
Karplus, M.1
McCammon, J.A.2
-
5
-
-
33646940952
-
Numerical-integration of cartesian equations of motion of a system with constraints - molecular-dynamics of N-alkanes
-
Ryckaert J.P., Ciccotti G., and Berendsen H.J.C. Numerical-integration of cartesian equations of motion of a system with constraints - molecular-dynamics of N-alkanes. J. Comput. Phys. 23 (1977) 327-341
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
6
-
-
20344362895
-
Revisiting and parallelizing SHAKE
-
Weinbach Y., and Elber R. Revisiting and parallelizing SHAKE. J. Comput. Phys. 209 (2005) 193-206
-
(2005)
J. Comput. Phys.
, vol.209
, pp. 193-206
-
-
Weinbach, Y.1
Elber, R.2
-
9
-
-
0020972782
-
Theoretical-studies of protein folding
-
Go N. Theoretical-studies of protein folding. Annu. Rev. Biophys. Bioeng. 12 (1983) 183-210
-
(1983)
Annu. Rev. Biophys. Bioeng.
, vol.12
, pp. 183-210
-
-
Go, N.1
-
10
-
-
0000355428
-
Respective roles of short-range and long-range interactions in protein folding
-
Go N., and Taketomi H. Respective roles of short-range and long-range interactions in protein folding. Proc. Natl. Acad. Sci. USA 75 (1978) 559-563
-
(1978)
Proc. Natl. Acad. Sci. USA
, vol.75
, pp. 559-563
-
-
Go, N.1
Taketomi, H.2
-
11
-
-
17044393884
-
Coarse-grained models for proteins
-
Tozzini V. Coarse-grained models for proteins. Curr. Opin. Struct. Biol. 15 (2005) 144-150
-
(2005)
Curr. Opin. Struct. Biol.
, vol.15
, pp. 144-150
-
-
Tozzini, V.1
-
12
-
-
10044243843
-
Generalized born model: analysis, refinement, and applications to proteins
-
Wojciechowski M., and Lesyng B. Generalized born model: analysis, refinement, and applications to proteins. J. Phys. Chem. B 108 (2004) 18368-18376
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 18368-18376
-
-
Wojciechowski, M.1
Lesyng, B.2
-
13
-
-
0141956090
-
Generalized born model with a simple smoothing function
-
Im W.P., Lee M.S., and Brooks C.L. Generalized born model with a simple smoothing function. J. Comput. Chem. 24 (2003) 1691-1702
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1691-1702
-
-
Im, W.P.1
Lee, M.S.2
Brooks, C.L.3
-
14
-
-
0037110472
-
Effective Born radii in the generalized Born approximation: the importance of being perfect
-
Onufriev A., Case D.A., and Bashford D. Effective Born radii in the generalized Born approximation: the importance of being perfect. J. Comput. Chem. 23 (2002) 1297-1304
-
(2002)
J. Comput. Chem.
, vol.23
, pp. 1297-1304
-
-
Onufriev, A.1
Case, D.A.2
Bashford, D.3
-
15
-
-
0033654297
-
Generalized born models of macromolecular solvation effects
-
Bashford D., and Case D.A. Generalized born models of macromolecular solvation effects. Annu. Rev. Phys. Chem. 51 (2000) 129-152
-
(2000)
Annu. Rev. Phys. Chem.
, vol.51
, pp. 129-152
-
-
Bashford, D.1
Case, D.A.2
-
16
-
-
20644449471
-
Modification of the generalized Born model suitable for macromolecules
-
Onufriev A., Bashford D., and Case D.A. Modification of the generalized Born model suitable for macromolecules. J. Phys. Chem. B 104 (2000) 3712-3720
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 3712-3720
-
-
Onufriev, A.1
Bashford, D.2
Case, D.A.3
-
17
-
-
0344778061
-
Semianalytical treatment of solvation for molecular mechanics and dynamics
-
Still W.C., Tempczyk A., Hawley R.C., and Hendrickson T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc. 112 (1990) 6127-6129
-
(1990)
J. Am. Chem. Soc.
, vol.112
, pp. 6127-6129
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.C.3
Hendrickson, T.4
-
20
-
-
0025294114
-
Conformational sampling using high-temperature molecular dynamics
-
Bruccoleri R.E., and Karplus M. Conformational sampling using high-temperature molecular dynamics. Biopolymers 29 (1990) 1847-1862
-
(1990)
Biopolymers
, vol.29
, pp. 1847-1862
-
-
Bruccoleri, R.E.1
Karplus, M.2
-
21
-
-
0025328145
-
Temperature dependence of the structure and dynamics of myoglobin. A simulation approach
-
Kuczera K., Kuriyan J., and Karplus M. Temperature dependence of the structure and dynamics of myoglobin. A simulation approach. J. Mol. Biol. 213 (1990) 351-373
-
(1990)
J. Mol. Biol.
, vol.213
, pp. 351-373
-
-
Kuczera, K.1
Kuriyan, J.2
Karplus, M.3
-
22
-
-
0037961507
-
Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. I. Formulation and benchmark test
-
Mitsutake A., Sugita Y., and Okamoto Y. Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. I. Formulation and benchmark test. J. Chem. Phys. 118 (2003) 6664-6675
-
(2003)
J. Chem. Phys.
, vol.118
, pp. 6664-6675
-
-
Mitsutake, A.1
Sugita, Y.2
Okamoto, Y.3
-
23
-
-
0037961506
-
Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. II. Application to a more complex system
-
Mitsutake A., Sugita Y., and Okamoto Y. Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. II. Application to a more complex system. J. Chem. Phys. 118 (2003) 6676-6688
-
(2003)
J. Chem. Phys.
, vol.118
, pp. 6676-6688
-
-
Mitsutake, A.1
Sugita, Y.2
Okamoto, Y.3
-
24
-
-
0001616080
-
Replica-exchange molecular dynamics method for protein folding
-
Sugita Y., and Okamoto Y. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 314 (1999) 141-151
-
(1999)
Chem. Phys. Lett.
, vol.314
, pp. 141-151
-
-
Sugita, Y.1
Okamoto, Y.2
-
25
-
-
0033688171
-
Temperature-accelerated dynamics for simulation of infrequent events
-
Sorensen M.R., and Voter A.F. Temperature-accelerated dynamics for simulation of infrequent events. J. Chem. Phys. 112 (2000) 9599-9606
-
(2000)
J. Chem. Phys.
, vol.112
, pp. 9599-9606
-
-
Sorensen, M.R.1
Voter, A.F.2
-
26
-
-
0030904524
-
Novel methods of sampling phase space in the simulation of biological systems
-
Berne B.J., and Straub J.E. Novel methods of sampling phase space in the simulation of biological systems. Curr. Opin. Struct. Biol. 7 (1997) 181-189
-
(1997)
Curr. Opin. Struct. Biol.
, vol.7
, pp. 181-189
-
-
Berne, B.J.1
Straub, J.E.2
-
27
-
-
0025600834
-
Enhanced sampling in molecular-dynamics - use of the time-dependent Hartree approximation for a simulation of carbon-monoxide diffusion through myoglobin
-
Elber R., and Karplus M. Enhanced sampling in molecular-dynamics - use of the time-dependent Hartree approximation for a simulation of carbon-monoxide diffusion through myoglobin. J. Am. Chem. Soc. 112 (1990) 9161-9175
-
(1990)
J. Am. Chem. Soc.
, vol.112
, pp. 9161-9175
-
-
Elber, R.1
Karplus, M.2
-
28
-
-
0000689085
-
Predicting slow structural transitions in macromolecular systems: conformational flooding
-
Grubmuller H. Predicting slow structural transitions in macromolecular systems: conformational flooding. Phys. Rev. E 52 (1995) 2893-2906
-
(1995)
Phys. Rev. E
, vol.52
, pp. 2893-2906
-
-
Grubmuller, H.1
-
29
-
-
0028710015
-
Local elevation: a method for improving the searching properties of molecular dynamics simulation
-
Huber T., Torda A.E., and van Gunsteren W.F. Local elevation: a method for improving the searching properties of molecular dynamics simulation. J. Comput. Aided. Mol. Des. 8 (1994) 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
-
30
-
-
0034737727
-
Leap-dynamics: efficient sampling of conformational space of proteins and peptides in solution
-
Kleinjung J., Bayley P., and Fraternali F. Leap-dynamics: efficient sampling of conformational space of proteins and peptides in solution. FEBS Lett. 470 (2000) 257-262
-
(2000)
FEBS Lett.
, vol.470
, pp. 257-262
-
-
Kleinjung, J.1
Bayley, P.2
Fraternali, F.3
-
31
-
-
0027794972
-
Targeted molecular-dynamics simulation of conformational change - application to the T - R transition in insulin
-
Schlitter J., Engels M., Kruger P., Jacoby E., and Wollmer A. Targeted molecular-dynamics simulation of conformational change - application to the T - R transition in insulin. Mol. Simul. 10 (1993) 291-308
-
(1993)
Mol. Simul.
, vol.10
, pp. 291-308
-
-
Schlitter, J.1
Engels, M.2
Kruger, P.3
Jacoby, E.4
Wollmer, A.5
-
32
-
-
0031144465
-
Hyperdynamics: accelerated molecular dynamics of infrequent events
-
Voter A.F. Hyperdynamics: accelerated molecular dynamics of infrequent events. Phys. Rev. Lett. 78 (1997) 3908-3911
-
(1997)
Phys. Rev. Lett.
, vol.78
, pp. 3908-3911
-
-
Voter, A.F.1
-
33
-
-
1442281293
-
A method for accelerating the molecular dynamics simulation of infrequent events
-
Voter A.F. A method for accelerating the molecular dynamics simulation of infrequent events. J. Chem. Phys. 106 (1997) 4665-4677
-
(1997)
J. Chem. Phys.
, vol.106
, pp. 4665-4677
-
-
Voter, A.F.1
-
34
-
-
0342929614
-
Non-physical sampling distributions in Monte-Carlo free-energy estimation - umbrella sampling
-
Torrie G.M., and Valleau J.P. Non-physical sampling distributions in Monte-Carlo free-energy estimation - umbrella sampling. J. Comput. Phys. 23 (1977) 187-199
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 187-199
-
-
Torrie, G.M.1
Valleau, J.P.2
-
35
-
-
36749113356
-
Monte-Carlo study of a phase-separating liquid-mixture by umbrella sampling
-
Torrie G.M., and Valleau J.P. Monte-Carlo study of a phase-separating liquid-mixture by umbrella sampling. J. Chem. Phys. 66 (1977) 1402-1408
-
(1977)
J. Chem. Phys.
, vol.66
, pp. 1402-1408
-
-
Torrie, G.M.1
Valleau, J.P.2
-
36
-
-
0001299795
-
Simple bias potential for boosting molecular dynamics with the hyperdynamics scheme
-
Steiner M.M., Genilloud P.A., and Wilkins J.W. Simple bias potential for boosting molecular dynamics with the hyperdynamics scheme. Phys. Rev. B 57 (1998) 10236-10239
-
(1998)
Phys. Rev. B
, vol.57
, pp. 10236-10239
-
-
Steiner, M.M.1
Genilloud, P.A.2
Wilkins, J.W.3
-
37
-
-
0037157282
-
Puddle-skimming: an efficient sampling of multidimensional configuration space
-
Rahman J.A., and Tully J.C. Puddle-skimming: an efficient sampling of multidimensional configuration space. J. Chem. Phys. 116 (2002) 8750-8760
-
(2002)
J. Chem. Phys.
, vol.116
, pp. 8750-8760
-
-
Rahman, J.A.1
Tully, J.C.2
-
38
-
-
0035106755
-
Accelerated molecular dynamics of rare events using the local boost method
-
art. no.-085403.
-
Wang J.C., Pal S., and Fichthorn K.A. Accelerated molecular dynamics of rare events using the local boost method. Phys. Rev. B 6308 (2001) art. no.-085403.
-
(2001)
Phys. Rev. B
, vol.6308
-
-
Wang, J.C.1
Pal, S.2
Fichthorn, K.A.3
-
39
-
-
0034289655
-
Atomistic simulation of the atomic structure and diffusion within the core region of an edge dislocation in aluminum
-
Fang Q.F., and Wang R. Atomistic simulation of the atomic structure and diffusion within the core region of an edge dislocation in aluminum. Phys. Rev. B 62 (2000) 9317-9324
-
(2000)
Phys. Rev. B
, vol.62
, pp. 9317-9324
-
-
Fang, Q.F.1
Wang, R.2
-
40
-
-
0033167047
-
Accelerated molecular dynamics of infrequent events
-
Pal S., and Fichthorn K.A. Accelerated molecular dynamics of infrequent events. Chem. Eng. J. 74 (1999) 77-83
-
(1999)
Chem. Eng. J.
, vol.74
, pp. 77-83
-
-
Pal, S.1
Fichthorn, K.A.2
-
41
-
-
0002976262
-
Hyper molecular dynamics with a local bias potential
-
Gong X.G., and Wilkins J.W. Hyper molecular dynamics with a local bias potential. Phys. Rev. B 59 (1999) 54-57
-
(1999)
Phys. Rev. B
, vol.59
, pp. 54-57
-
-
Gong, X.G.1
Wilkins, J.W.2
-
42
-
-
3142716857
-
Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules
-
Hamelberg D., Mongan J., and McCammon J.A. Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules. J. Chem. Phys. 120 (2004) 11919-11929
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 11919-11929
-
-
Hamelberg, D.1
Mongan, J.2
McCammon, J.A.3
-
43
-
-
13644250683
-
Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine-proline motifs: accelerated molecular dynamics analysis
-
Hamelberg D., Shen T., and McCammon J.A. Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine-proline motifs: accelerated molecular dynamics analysis. J. Am. Chem. Soc. 127 (2005) 1969-1974
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 1969-1974
-
-
Hamelberg, D.1
Shen, T.2
McCammon, J.A.3
-
44
-
-
22544433172
-
Relating kinetic rates and local energetic roughness by accelerated molecular-dynamics simulations
-
Hamelberg D., Shen T., and McCammon J.A. Relating kinetic rates and local energetic roughness by accelerated molecular-dynamics simulations. J. Chem. Phys. 122 (2005) 241103
-
(2005)
J. Chem. Phys.
, vol.122
, pp. 241103
-
-
Hamelberg, D.1
Shen, T.2
McCammon, J.A.3
-
45
-
-
0024121530
-
Diffusion in a rough potential
-
Zwanzig R. Diffusion in a rough potential. Proc. Natl. Acad. Sci. USA 85 (1988) 2029-2030
-
(1988)
Proc. Natl. Acad. Sci. USA
, vol.85
, pp. 2029-2030
-
-
Zwanzig, R.1
|