-
1
-
-
0033723528
-
Femtochemistry: Atomic-scale dynamics of the chemical bond Zewail A H. 2000
-
10.1021/jp001460h 1:CAS:528:DC%2BD3cXktVeisbY%3D
-
A.H. Zewail 2000 Femtochemistry: Atomic-scale dynamics of the chemical bond Zewail A H. 2000 J Phys Chem A 104 5660 5694 10.1021/jp001460h 1:CAS:528:DC%2BD3cXktVeisbY%3D
-
(2000)
J Phys Chem A
, vol.104
, pp. 5660-5694
-
-
Zewail, A.H.1
-
2
-
-
0031688282
-
Enzymatic transition states and transition state analog design
-
DOI 10.1146/annurev.biochem.67.1.693
-
V.L. Schramm 1998 Enzymatic transition states and transition state analog design Ann Rev Biochem 67 693 720 10.1146/annurev.biochem.67.1.693 1:CAS:528:DyaK1cXlsFOmsbg%3D (Pubitemid 28411142)
-
(1998)
Annual Review of Biochemistry
, vol.67
, pp. 693-720
-
-
Schramm, V.L.1
-
4
-
-
0024578173
-
Free-energy via molecular simulation-applications to chemical and biomolecular systems
-
10.1146/annurev.bb.18.060189.002243 1:CAS:528:DyaL1MXlvVajsLs%3D
-
D.L. Beveridge 1989 Free-energy via molecular simulation-applications to chemical and biomolecular systems Ann Rev Biophys Biophys Chem 18 431 492 10.1146/annurev.bb.18.060189.002243 1:CAS:528:DyaL1MXlvVajsLs%3D
-
(1989)
Ann Rev Biophys Biophys Chem
, vol.18
, pp. 431-492
-
-
Beveridge, D.L.1
-
5
-
-
51349113036
-
Crim, Chemical reaction dynamics
-
Crim, Chemical reaction dynamics. Proc Natl Acad Sci USA, 2008, 105(35): 12647-12648
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, Issue.35
, pp. 12647-12648
-
-
-
6
-
-
0001626776
-
Adaptive umbrella sampling: Self-consistent determination of the non-boltzmann bias
-
10.1016/0021-9991(87)90054-4
-
M. Mezei 1987 Adaptive umbrella sampling: self-consistent determination of the non-boltzmann bias J Comput Phys 68 237 248 10.1016/0021-9991(87)90054-4
-
(1987)
J Comput Phys
, vol.68
, pp. 237-248
-
-
Mezei, M.1
-
8
-
-
0342929614
-
Nonphysical sampling distributions in monte carlo free-energy estimation: Umbrella sampling
-
10.1016/0021-9991(77)90121-8
-
G.M. Torrie J.P. Valleau 1977 Nonphysical sampling distributions in monte carlo free-energy estimation: umbrella sampling J Comp Phys 23 187 199 10.1016/0021-9991(77)90121-8
-
(1977)
J Comp Phys
, vol.23
, pp. 187-199
-
-
Torrie, G.M.1
Valleau, J.P.2
-
9
-
-
0035935802
-
Calculating free energies using average force
-
DOI 10.1063/1.1410978
-
E. Darve A. Pohorille 2001 Calculating free energies using average force J Chem Phys 115 20 9169 9183 10.1063/1.1410978 1:CAS:528:DC%2BD3MXotlyis7c%3D (Pubitemid 33128021)
-
(2001)
Journal of Chemical Physics
, vol.115
, Issue.20
, pp. 9169-9183
-
-
Darve, E.1
Pohorille, A.2
-
10
-
-
42149194240
-
Adaptive biasing force method for scalar and vector free energy calculations
-
DOI 10.1063/1.2829861
-
E. Darve D. Rodríguez-Gómez A. Pohorille 2008 Adaptive biasing force method for scalar and vector free energy calculations J Chem Phys 128 144120 10.1063/1.2829861 (Pubitemid 351537156)
-
(2008)
Journal of Chemical Physics
, vol.128
, Issue.14
, pp. 144120
-
-
Darve, E.1
Rodriguez-Gomez, D.2
Pohorille, A.3
-
11
-
-
0033577284
-
Calculation of the Ramachandran potential of mean force for a disaccharide in aqueous solution
-
DOI 10.1021/ja9821596
-
K.J. Naidoo J.W. Brady 1999 Calculation of the ramachandran potential of mean force for a disaccharide in aqueous solution J Am Chem Soc 121 10 2244 2252 10.1021/ja9821596 1:CAS:528:DyaK1MXht1artr4%3D (Pubitemid 29152438)
-
(1999)
Journal of the American Chemical Society
, vol.121
, Issue.10
, pp. 2244-2252
-
-
Naidoo, K.J.1
Brady, J.W.2
-
12
-
-
4243819810
-
New monte carlo technique for studying phase transitions
-
10.1103/PhysRevLett.61.2635 1:CAS:528:DyaL1MXht1Wmu7s%3D
-
A.M. Ferrenberg R.H. Swendsen 1988 New monte carlo technique for studying phase transitions Phys Rev Lett 61 23 2635 2638 10.1103/PhysRevLett.61.2635 1:CAS:528:DyaL1MXht1Wmu7s%3D
-
(1988)
Phys Rev Lett
, vol.61
, Issue.23
, pp. 2635-2638
-
-
Ferrenberg, A.M.1
Swendsen, R.H.2
-
13
-
-
0036771632
-
Carbohydrate solution simulations: Producing a force field with experimentally consistent primary alcohol rotational frequencies and populations
-
DOI 10.1002/jcc.10119
-
M.M. Kuttel J.W. Brady K.J. Naidoo 2002 Carbohydrate solution simulations: Producing a force field with experimentally consistent primary alcohol rotational frequencies and populations J Comp Chem 23 13 1236 1243 10.1002/jcc.10119 1:CAS:528:DC%2BD38XmsVKgsL0%3D (Pubitemid 35017037)
-
(2002)
Journal of Computational Chemistry
, vol.23
, Issue.13
, pp. 1236-1243
-
-
Kuttel, M.1
Brady, J.W.2
Naidoo, K.J.3
-
14
-
-
18144409112
-
Free energy surfaces for the α(1 × 4)-glycosidic linkage: Implications for polysaccharide solution structure and dynamics
-
DOI 10.1021/jp044756m
-
M.M. Kuttel K.J. Naidoo 2005 Free energy surfaces for the alpha(1-4)-glycosidic linkage: Implications for polysaccharide solution structure and dynamics J Phys Chem B 109 7468 7474 10.1021/jp044756m 1:CAS:528:DC%2BD2MXislWlsbw%3D (Pubitemid 40609881)
-
(2005)
Journal of Physical Chemistry B
, vol.109
, Issue.15
, pp. 7468-7474
-
-
Kuttel, M.M.1
Naidoo, K.J.2
-
15
-
-
0141887118
-
Implementation of an adaptive umbrella sampling method for the calculation of multidimensional potential of mean force of chemical reactions in solution
-
10.1002/jcc.10315 1:CAS:528:DC%2BD3sXosFOhu7w%3D
-
R. Rajamani K.J. Naidoo J. Gao 2003 Implementation of an adaptive umbrella sampling method for the calculation of multidimensional potential of mean force of chemical reactions in solution J Comp Chem 24 1775 1781 10.1002/jcc.10315 1:CAS:528:DC%2BD3sXosFOhu7w%3D
-
(2003)
J Comp Chem
, vol.24
, pp. 1775-1781
-
-
Rajamani, R.1
Naidoo, K.J.2
Gao, J.3
-
16
-
-
68249147647
-
Free Energies from Adaptive Reaction Coordinate Forces (FEARCF): An application to ring puckering
-
10.1080/00268970902852608 1:CAS:528:DC%2BD1MXotlWks7g%3D
-
C.B. Barnett K.J. Naidoo 2009 Free Energies from Adaptive Reaction Coordinate Forces (FEARCF): An application to ring puckering Mol Phys 107 8-12 1243 1250 10.1080/00268970902852608 1:CAS:528:DC%2BD1MXotlWks7g%3D
-
(2009)
Mol Phys
, vol.107
, Issue.812
, pp. 1243-1250
-
-
Barnett, C.B.1
Naidoo, K.J.2
-
17
-
-
76149141189
-
Computing free energy hypersurfaces for anisotropic intermolecular associations
-
J. Strümpfer K.J. Naidoo 2010 Computing free energy hypersurfaces for anisotropic intermolecular associations J Comp Chem 31 2 308 316
-
(2010)
J Comp Chem
, vol.31
, Issue.2
, pp. 308-316
-
-
Strümpfer, J.1
Naidoo, K.J.2
-
18
-
-
6644221271
-
Efficient, multiple-range random walk algorithm to calculate the density of states
-
DOI 10.1103/PhysRevLett.86.2050
-
F.G. Wang D.P. Landau 2001 Efficient, multiple-range random walk algorithm to calculate the density of states Phys Rev Lett 86 10 2050 2053 10.1103/PhysRevLett.86.2050 1:CAS:528:DC%2BD3MXhsFGnu7s%3D (Pubitemid 32254758)
-
(2001)
Physical Review Letters
, vol.86
, Issue.10
, pp. 2050-2053
-
-
Wang, F.1
Landau, D.P.2
-
19
-
-
39749147672
-
Determining the density of states for classical statistical models: A random walk algorithm to produce a flat histogram
-
Wang FG, Landau DP. Determining the density of states for classical statistical models: A random walk algorithm to produce a flat histogram. Phys Rev E, 2001, 64(5)
-
(2001)
Phys Rev e
, vol.64
, Issue.5
-
-
Wang, F.G.1
Landau, D.P.2
-
20
-
-
0036790894
-
Escaping free-energy minima
-
10.1073/pnas.202427399 1:CAS:528:DC%2BD38XnvFGiurc%3D
-
A. Laio M. Parrinello 2002 Escaping free-energy minima Proc Natl Acad Sci 99 20 12562 12566 10.1073/pnas.202427399 1:CAS:528:DC%2BD38XnvFGiurc%3D
-
(2002)
Proc Natl Acad Sci
, vol.99
, Issue.20
, pp. 12562-12566
-
-
Laio, A.1
Parrinello, M.2
-
21
-
-
0000307978
-
Sodium chloride ion pair interaction in water:computer simulation
-
10.1016/0009-2614(84)85660-2 1:CAS:528:DyaL2cXitFKltro%3D
-
M. Berkowitz O.A. Karim J.A. McCammon P.J. Rossky 1984 Sodium chloride ion pair interaction in water:computer simulation Chem Phys Lett 105 6 577 580 10.1016/0009-2614(84)85660-2 1:CAS:528:DyaL2cXitFKltro%3D
-
(1984)
Chem Phys Lett
, vol.105
, Issue.6
, pp. 577-580
-
-
Berkowitz, M.1
Karim, O.A.2
McCammon, J.A.3
Rossky, P.J.4
-
22
-
-
0001362721
-
Solvation structure of a sodium chloride ion pair in water
-
10.1021/ja00268a007 1:CAS:528:DyaL28XhsFKkurw%3D
-
A.C. Belch M. Berkowitz J.A. McCammon 1986 Solvation structure of a sodium chloride ion pair in water J Am Chem Soc 108 1755 1761 10.1021/ja00268a007 1:CAS:528:DyaL28XhsFKkurw%3D
-
(1986)
J Am Chem Soc
, vol.108
, pp. 1755-1761
-
-
Belch, A.C.1
Berkowitz, M.2
McCammon, J.A.3
-
23
-
-
33846406882
-
A comparison of methods to compute the potential of mean force
-
10.1002/cphc.200600527 1:CAS:528:DC%2BD2sXpsFSktA%3D%3D
-
D. Trzesniak A.P.E. Kunz W.F. van Gunsteren 2007 A comparison of methods to compute the potential of mean force Chemphyschem 8 1 162 169 10.1002/cphc.200600527 1:CAS:528:DC%2BD2sXpsFSktA%3D%3D
-
(2007)
Chemphyschem
, vol.8
, Issue.1
, pp. 162-169
-
-
Trzesniak, D.1
Kunz, A.P.E.2
Van Gunsteren, W.F.3
-
24
-
-
38849144001
-
Computing accurate potentials of mean force in electrolyte solutions with the generalized gradient-augmented harmonic Fourier beads method
-
DOI 10.1063/1.2825620
-
I.V. Khavrutskii J. Dzubiella J.A. McCammon 2008 Computing accurate potentials of mean force in electrolyte solutions with the generalized gradient-augmented harmonic Fourier beads method J Chem Phys 128 4 044106 044113 10.1063/1.2825620 (Pubitemid 351191586)
-
(2008)
Journal of Chemical Physics
, vol.128
, Issue.4
, pp. 044106
-
-
Khavrutskii, I.V.1
Dzubiella, J.2
McCammon, J.A.3
-
25
-
-
4344606960
-
Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations
-
C. Bartels M. Karplus 1997 Multidimensional adaptive umbrella sampling: applications to main chain and side chain peptide conformation J Comp Chem 18 12 1450 1462 10.1002/(SICI)1096-987X(199709)18:12<1450::AID-JCC3>3.0.CO;2-I 1:CAS:528:DyaK2sXlvV2nu7s%3D (Pubitemid 127637343)
-
(1997)
Journal of Computational Chemistry
, vol.18
, Issue.12
, pp. 1450-1462
-
-
Bartels, C.1
Karplus, M.2
-
26
-
-
0031648813
-
Probability distributions for complex systems: Adaptive umbrella sampling of the potential energy
-
C. Bartels M. Karplus 1998 Probability distributions for complex systems: Adaptive umbrella sampling of the potential energy J Phys Chem B 102 865 880 10.1021/jp972280j 1:CAS:528:DyaK1cXivFSjsA%3D%3D (Pubitemid 128600624)
-
(1998)
Journal of Physical Chemistry B
, vol.102
, Issue.5
, pp. 865-880
-
-
Bartels, C.1
Karplus, M.2
-
27
-
-
0000656482
-
Efficient Monte Carlo methods for the computer simulation of biological molecules
-
10.1103/PhysRevA.45.8894 1:CAS:528:DyaK38XltVOktr4%3D
-
D. Bouzida S. Kumar R.H. Swendsen 1992 Efficient Monte Carlo methods for the computer simulation of biological molecules Phys Rev A 45 12 8894 10.1103/PhysRevA.45.8894 1:CAS:528:DyaK38XltVOktr4%3D
-
(1992)
Phys Rev A
, vol.45
, Issue.12
, pp. 8894
-
-
Bouzida, D.1
Kumar, S.2
Swendsen, R.H.3
-
28
-
-
84986519238
-
The Weighted Histogram analysis method for free-energy calculations on biomolecules
-
1:CAS:528:DyaK38XmtVynsrs%3D
-
S. Kumar D. Bouzida R.H. Swendsen P.A. Kollman J.M. Rosenberg 1992 The Weighted Histogram analysis method for free-energy calculations on biomolecules I. The Method. J Comput Chem 13 1011 1021 1:CAS:528:DyaK38XmtVynsrs%3D
-
(1992)
I. The Method. J Comput Chem
, vol.13
, pp. 1011-1021
-
-
Kumar, S.1
Bouzida, D.2
Swendsen, R.H.3
Kollman, P.A.4
Rosenberg, J.M.5
-
29
-
-
0001186767
-
Method for free-energy calculations using iterative techniques
-
S. Kumar P.W. Payne M. Vasquez 1996 Method for free-energy calculations using iterative techniques J Comput Chem 17 10 1269 1275 10.1002/(SICI)1096- 987X(19960730)17:10<1269::AID-JCC7>3.0.CO;2-M 1:CAS:528:DyaK28Xjslyrs74%3D (Pubitemid 126562032)
-
(1996)
Journal of Computational Chemistry
, vol.17
, Issue.10
, pp. 1269-1275
-
-
Kumar, S.1
Payne, P.W.2
Vasquez, M.3
-
30
-
-
33646987405
-
Optimized monte carlo data analysis
-
10.1103/PhysRevLett.63.1195 1:CAS:528:DyaL1MXmtFeqs70%3D
-
A.M. Ferrenberg R.H. Swendsen 1989 Optimized monte carlo data analysis Phys Rev Lett 63 12 1195 1198 10.1103/PhysRevLett.63.1195 1:CAS:528: DyaL1MXmtFeqs70%3D
-
(1989)
Phys Rev Lett
, vol.63
, Issue.12
, pp. 1195-1198
-
-
Ferrenberg, A.M.1
Swendsen, R.H.2
-
31
-
-
0001114361
-
Determination of equilibrium properties of biomolecular systems using multidimensional adaptive umbrella sampling
-
C. Bartels M. Schaefer M. Karplus 1999 Determination of equilibrium properties of biomolecular systems using multidimentional adaptive umbrella sampling J Chem Phys 111 178 8048 8067 10.1063/1.480139 1:CAS:528: DyaK1MXms1equrc%3D (Pubitemid 129579632)
-
(1999)
Journal of Chemical Physics
, vol.111
, Issue.17
, pp. 8048-8067
-
-
Bartels, C.1
Schaefer, M.2
Karplus, M.3
-
32
-
-
84986497803
-
Multidimensional free-energy calculations using the weighted histo-gram analysis method
-
10.1002/jcc.540161104 1:CAS:528:DyaK2MXovVKqtrg%3D
-
S. Kumar J.M. Rosenberg D. Bouzida R.H. Swendsen P.A. Kollman 1995 Multidimensional free-energy calculations using the weighted histo-gram analysis method J Comput Chem 16 11 1339 1350 10.1002/jcc.540161104 1:CAS:528: DyaK2MXovVKqtrg%3D
-
(1995)
J Comput Chem
, vol.16
, Issue.11
, pp. 1339-1350
-
-
Kumar, S.1
Rosenberg, J.M.2
Bouzida, D.3
Swendsen, R.H.4
Kollman, P.A.5
-
33
-
-
0023318418
-
Sidechain rotational isomerization in proteins: Dynamic simulation with solvent surroundings
-
10.1016/S0006-3495(87)83388-X 1:CAS:528:DyaL2sXksFCltL8%3D
-
I. Ghosh J.A. McCammon 1987 Sidechain rotational isomerization in proteins: dynamic simulation with solvent surroundings Biophys J 51 637 641 10.1016/S0006-3495(87)83388-X 1:CAS:528:DyaL2sXksFCltL8%3D
-
(1987)
Biophys J
, vol.51
, pp. 637-641
-
-
Ghosh, I.1
McCammon, J.A.2
-
34
-
-
28444443140
-
MD simulations and Poincare recurrence time
-
10.1007/BF01013169
-
S.K. Ma 1981 MD simulations and Poincare recurrence time J Stat Phys 26 221 10.1007/BF01013169
-
(1981)
J Stat Phys
, vol.26
, pp. 221
-
-
Ma, S.K.1
-
35
-
-
67650500988
-
CHARMM: The biomolecular simulation program
-
10.1002/jcc.21287 1:CAS:528:DC%2BD1MXms1Ciu70%3D
-
B.R. Brooks C.L. Brooks A.D. Mackerell Jr. L. Nilsson R.J. Petrella B. Roux Y. Won G. Archontis C. Bartels S. Boresch A. Caflisch L. Caves Q. Cui A.R. Dinner M. Feig S. Fischer J. Gao M. Hodoscek W. Im K. Kuczera T. Lazaridis J. Ma V. Ovchinnikov E. Paci R.W. Pastor C.B. Post J.Z. Pu M. Schaefer B. Tidor R.M. Venable H.L. Woodcock X. Wu W. Yang D.M. York M. Karplus 2009 CHARMM: The biomolecular simulation program J Comp Chem 30 10 1545 1614 10.1002/jcc.21287 1:CAS:528:DC%2BD1MXms1Ciu70%3D
-
(2009)
J Comp Chem
, vol.30
, Issue.10
, pp. 1545-1614
-
-
Brooks, B.R.1
Brooks, C.L.2
Mackerell Jr., A.D.3
Nilsson, L.4
Petrella, R.J.5
Roux, B.6
Won, Y.7
Archontis, G.8
Bartels, C.9
Boresch, S.10
Caflisch, A.11
Caves, L.12
Cui, Q.13
Dinner, A.R.14
Feig, M.15
Fischer, S.16
Gao, J.17
Hodoscek, M.18
Im, W.19
Kuczera, K.20
Lazaridis, T.21
Ma, J.22
Ovchinnikov, V.23
Paci, E.24
Pastor, R.W.25
Post, C.B.26
Pu, J.Z.27
Schaefer, M.28
Tidor, B.29
Venable, R.M.30
Woodcock, H.L.31
Wu, X.32
Yang, W.33
York, D.M.34
Karplus, M.35
more..
-
37
-
-
0017100947
-
Theoretical studies of enzymic reactions-dielectric, electrostatic and steric stabilization of carbonium-ion in reaction of lysozyme
-
10.1016/0022-2836(76)90311-9 1:CAS:528:DyaE28XktFKhtr0%3D
-
A. Warshel M. Levitt 1976 Theoretical studies of enzymic reactions-dielectric, electrostatic and steric stabilization of carbonium-ion in reaction of lysozyme J Mol Biol 103 227 10.1016/0022-2836(76)90311-9 1:CAS:528:DyaE28XktFKhtr0%3D
-
(1976)
J Mol Biol
, vol.103
, pp. 227
-
-
Warshel, A.1
Levitt, M.2
-
38
-
-
33845283509
-
Free energy pertubation method for chemical reactions in the condensed phase: A dynamical approach based on the combined quantum and molecular mechanical potential
-
10.1021/ja00260a028 1:CAS:528:DyaL1cXltlCh
-
P. Bash M. Fields M. Karplus 1987 Free energy pertubation method for chemical reactions in the condensed phase: A dynamical approach based on the combined quantum and molecular mechanical potential J Am Chem Soc 109 26 8092 8094 10.1021/ja00260a028 1:CAS:528:DyaL1cXltlCh
-
(1987)
J Am Chem Soc
, vol.109
, Issue.26
, pp. 8092-8094
-
-
Bash, P.1
Fields, M.2
Karplus, M.3
-
39
-
-
84986513644
-
A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations
-
10.1002/jcc.540110605 1:CAS:528:DyaK3cXlt1Sqtrk%3D
-
M.J. Field P.A. Bash M. Karplus 1990 A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations J Comput Chem 11 6 700 733 10.1002/jcc.540110605 1:CAS:528:DyaK3cXlt1Sqtrk%3D
-
(1990)
J Comput Chem
, vol.11
, Issue.6
, pp. 700-733
-
-
Field, M.J.1
Bash, P.A.2
Karplus, M.3
-
41
-
-
85021615308
-
Development and use of quantum mechanical molecular models. 76. AM1: A new general purpose quantum mechanical molecular model. [Erratum to document cited in CA103(2):11627f]
-
10.1021/ja00065a078
-
E.H. Yonemoto R.L. Riley Y. Kim II S.J. Atherton R.H. Schmehl T.E. Mallouk 1993 Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model. [Erratum to document cited in CA103(2):11627f] J Am Chem Soc 115 12 5348 10.1021/ja00065a078
-
(1993)
J Am Chem Soc
, vol.115
, Issue.12
, pp. 5348
-
-
Yonemoto, E.H.1
Riley, R.L.2
Kim, I.I.Y.3
Atherton, S.J.4
Schmehl, R.H.5
Mallouk, T.E.6
-
42
-
-
84988129057
-
Optimization of parameters for semiempirical methods. I. Method
-
10.1002/jcc.540100208 1:CAS:528:DyaL1MXkt1ylu70%3D
-
J.J.P. Stewart 1989 Optimization of parameters for semiempirical methods. I. Method J Comput Chem 10 2 209 220 10.1002/jcc.540100208 1:CAS:528: DyaL1MXkt1ylu70%3D
-
(1989)
J Comput Chem
, vol.10
, Issue.2
, pp. 209-220
-
-
Stewart, J.J.P.1
-
43
-
-
4143118105
-
Towards a quantum mechanical force field for carbohydrates: A reparametrized semi-empirical MO approach
-
10.1016/j.cplett.2004.07.037 1:CAS:528:DC%2BD2cXmsVajsb4%3D
-
J.P. McNamara A.M. Muslim H. Abdel-Aal H. Wang M. Mohr I.H. Hillier R.A. Bryce 2004 Towards a quantum mechanical force field for carbohydrates: A reparametrized semi-empirical MO approach Chem Phys Lett 394 429 436 10.1016/j.cplett.2004.07.037 1:CAS:528:DC%2BD2cXmsVajsb4%3D
-
(2004)
Chem Phys Lett
, vol.394
, pp. 429-436
-
-
McNamara, J.P.1
Muslim, A.M.2
Abdel-Aal, H.3
Wang, H.4
Mohr, M.5
Hillier, I.H.6
Bryce, R.A.7
-
44
-
-
57949100084
-
Stereoelectronic and solvation effects deter-mine hydroxymethyl conformational preferences in monosaccharides
-
10.1021/jp8067409 1:CAS:528:DC%2BD1cXhtlemt73I
-
C.B. Barnett K.J. Naidoo 2008 Stereoelectronic and solvation effects deter-mine hydroxymethyl conformational preferences in monosaccharides J Phys Chem B 112 15450 15459 10.1021/jp8067409 1:CAS:528:DC%2BD1cXhtlemt73I
-
(2008)
J Phys Chem B
, vol.112
, pp. 15450-15459
-
-
Barnett, C.B.1
Naidoo, K.J.2
-
45
-
-
0035138648
-
QM/MM implementation of the self-consistent charge density functional tight binding (SCC-DFTB) method
-
DOI 10.1021/jp0029109
-
Q. Cui M. Elstner E. Kaxiras T. Frauenheim M. Karplus 2001 A QM/MM implementation of the self-consistent charge density functional tight binding (SCC-DFTB) method J Phys Chem B 105 569 585 10.1021/jp0029109 1:CAS:528:DC%2BD3cXovVCisL4%3D (Pubitemid 32159216)
-
(2001)
Journal of Physical Chemistry B
, vol.105
, Issue.2
, pp. 569-585
-
-
Cui, Q.1
Elstner, M.2
Kaxiras, E.3
Frauenheim, T.4
Karplus, M.5
-
47
-
-
0029633155
-
The calculation of the potential of mean force using computer simulations
-
10.1016/0010-4655(95)00053-I 1:CAS:528:DyaK2MXps1Wrt7o%3D
-
B. Roux 1995 The calculation of the potential of mean force using computer simulations Comput Phys Comm 91 1-3 275 282 10.1016/0010-4655(95)00053- I 1:CAS:528:DyaK2MXps1Wrt7o%3D
-
(1995)
Comput Phys Comm
, vol.91
, Issue.13
, pp. 275-282
-
-
Roux, B.1
-
49
-
-
41849123553
-
Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis
-
DOI 10.1021/ja0759141
-
K.H. Nam J.L. Gao D.M. York 2008 Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis J Am Chem Soc 130 14 4680 4691 10.1021/ja0759141 1:CAS:528:DC%2BD1cXjsVWgs78%3D (Pubitemid 351500104)
-
(2008)
Journal of the American Chemical Society
, vol.130
, Issue.14
, pp. 4680-4691
-
-
Nam, K.1
Gao, J.2
York, D.M.3
-
50
-
-
67849085413
-
Critical role of substrate conformational change in the proton transfer process catalyzed by 4-oxalocrotonate tautomerase
-
10.1021/ja8087423 1:CAS:528:DC%2BD1MXhsFSltLc%3D
-
J.J. Ruiz-Pernia M. Garcia-Viloca S. Bhattacharyya J. Gao D.G. Truhlar 2009 Critical role of substrate conformational change in the proton transfer process catalyzed by 4-oxalocrotonate tautomerase J Am Chem Soc 131 7 2687 2698 10.1021/ja8087423 1:CAS:528:DC%2BD1MXhsFSltLc%3D
-
(2009)
J Am Chem Soc
, vol.131
, Issue.7
, pp. 2687-2698
-
-
Ruiz-Pernia, J.J.1
Garcia-Viloca, M.2
Bhattacharyya, S.3
Gao, J.4
Truhlar, D.G.5
-
51
-
-
35948986438
-
Molecular dynamics simulations of the catalytic pathway of a cysteine protease: A combined QM/MM study of human cathepsin K
-
DOI 10.1021/ja074222+
-
S. Ma L.S. Devi-Kesavan J. Gao 2007 Molecular dynamics simulations of the catalytic pathway of a cysteine protease: A combined QM/MM study of human cathepsin K J Am Chem Soc 129 44 13633 13645 10.1021/ja074222+ 1:CAS:528:DC%2BD2sXhtFKhtbjK (Pubitemid 350071792)
-
(2007)
Journal of the American Chemical Society
, vol.129
, Issue.44
, pp. 13633-13645
-
-
Ma, S.1
Devi-Kesavan, L.S.2
Gao, J.3
-
52
-
-
0037865396
-
Mapping the conformational itinerary of β-glycosidases by X-ray crystallography
-
DOI 10.1042/BST0310523
-
G.J. Davies V.M.A. Ducros A. Varrot D.L. Zechel 2003 Mapping the conformational itinerary of beta-glycosidases by X-ray crystallography Biochemical Society Transactions 31 523 527 10.1042/BST0310523 1:CAS:528:DC%2BD3sXktF2isbo%3D (Pubitemid 36750724)
-
(2003)
Biochemical Society Transactions
, vol.31
, Issue.3
, pp. 523-527
-
-
Davies, G.J.1
Ducros, V.M.-A.2
Varrot, A.3
Zechel, D.L.4
-
53
-
-
0034826966
-
The conformational origin of the barrier to the formation of neighboring group assistance in glycosylation reactions: A dynamical Density Functional Theory study
-
DOI 10.1021/ja001194l
-
A. Berces G. Enright T. Nukada D.M. Whitfield 2001 The conformational origin of the barrier to the formation of neighboring group assistance in glycosylation reactions: A dynamical density functional theory study J Am Chem Soc 123 5460 5464 10.1021/ja001194l 1:CAS:528:DC%2BD3MXjsVOktr0%3D (Pubitemid 32888514)
-
(2001)
Journal of the American Chemical Society
, vol.123
, Issue.23
, pp. 5460-5464
-
-
Berces, A.1
Enright, G.2
Nukada, T.3
Whitfield, D.M.4
-
54
-
-
1842692143
-
A general definition of Ring Puckering Coordinates
-
10.1021/ja00839a011
-
D. Cremer J.A. Pople 1975 A general definition of Ring Puckering Coordinates J Am Chem Soc 96 6 1354 1358 10.1021/ja00839a011
-
(1975)
J Am Chem Soc
, vol.96
, Issue.6
, pp. 1354-1358
-
-
Cremer, D.1
Pople, J.A.2
-
55
-
-
34250866873
-
Puckering coordinates of monocyclic rings by triangular decomposition
-
DOI 10.1021/ci600492e
-
A.D. Hill P.J. Reilly 2007 Puckering coordinates of monocyclic rings by triangular decomposition J Chem Inf Model 47 3 1031 1035 10.1021/ci600492e 1:CAS:528:DC%2BD2sXivF2js74%3D (Pubitemid 46973718)
-
(2007)
Journal of Chemical Information and Modeling
, vol.47
, Issue.3
, pp. 1031-1035
-
-
Hill, A.D.1
Reilly, P.J.2
-
57
-
-
79952773605
-
Ring puckering: A metric for evaluating the accuracy of AM1, PM3, PM3CARB-1 and SCC-DFTB carbohydrate QM/MM simulations
-
10.1021/jp107620h 1:CAS:528:DC%2BC3cXhsFaksb3K
-
C.B. Barnett K.J. Naidoo 2010 Ring puckering: A metric for evaluating the accuracy of AM1, PM3, PM3CARB-1 and SCC-DFTB carbohydrate QM/MM simulations J Phys Chem B 114 17142 17154 10.1021/jp107620h 1:CAS:528:DC%2BC3cXhsFaksb3K
-
(2010)
J Phys Chem B
, vol.114
, pp. 17142-17154
-
-
Barnett, C.B.1
Naidoo, K.J.2
-
58
-
-
35948946987
-
Extension of the self-consistent-charge density-functional tight-binding method: Third-order expansion of the density functional theory total energy and introduction of a modified effective coulomb interaction
-
DOI 10.1021/jp074167r
-
Y. Yang H. Yu D. York Q. Cui M. Elstner 2007 Extension of the self-consistent-charge density-functional tight-binding method: third-order expansion of the density functional theory total energy and introduction of a modified effective coulomb interaction J Phys Chem A 111 10861 10873 10.1021/jp074167r 1:CAS:528:DC%2BD2sXhtFSmtr%2FI (Pubitemid 350064055)
-
(2007)
Journal of Physical Chemistry A
, vol.111
, Issue.42
, pp. 10861-10873
-
-
Yang, Y.1
Yu, H.2
York, D.3
Cui, Q.4
Elstner, M.5
-
60
-
-
77956642470
-
Pyranose ring transition state is derived from cellobiohydrolase i induced conformational stability and glycosidic bond polarization
-
10.1021/ja103766w 1:CAS:528:DC%2BC3cXhtVOqtLzE
-
C.B. Barnett K.A. Wilkinson K.J. Naidoo 2010 Pyranose ring transition state is derived from cellobiohydrolase I induced conformational stability and glycosidic bond polarization J Am Chem Soc 132 37 12800 12803 10.1021/ja103766w 1:CAS:528:DC%2BC3cXhtVOqtLzE
-
(2010)
J Am Chem Soc
, vol.132
, Issue.37
, pp. 12800-12803
-
-
Barnett, C.B.1
Wilkinson, K.A.2
Naidoo, K.J.3
-
61
-
-
82555187189
-
Molecular details from computational reaction dynamics for the Cellobidrydrolase i glycosylation reaction
-
doi: 10.1021/ja206842j
-
Barnett CB, Wilkinson KA, Naidoo KJ. Molecular details from computational reaction dynamics for the Cellobidrydrolase I glycosylation reaction. J Am Chem Soc, 2011, doi: 10.1021/ja206842j
-
(2011)
J Am Chem Soc
-
-
Barnett, C.B.1
Wilkinson, K.A.2
Naidoo, K.J.3
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