-
1
-
-
0036273082
-
Bacterial detoxification of organophosphate nerve agents
-
Raushel, F. M. (2002) Bacterial detoxification of organophosphate nerve agents, Curr. Opin. Microbiol. 5, 288-295.
-
(2002)
Curr. Opin. Microbiol
, vol.5
, pp. 288-295
-
-
Raushel, F.M.1
-
2
-
-
0029923114
-
Molecular aspects of pesticide degradation by microorganisms
-
Kumar, S., Mukerji, K. G., and Lai, R. (1996) Molecular aspects of pesticide degradation by microorganisms, Crit. Rev. Microbiol. 22, 1-26.
-
(1996)
Crit. Rev. Microbiol
, vol.22
, pp. 1-26
-
-
Kumar, S.1
Mukerji, K.G.2
Lai, R.3
-
3
-
-
33748366780
-
Effective countermeasure against poisoning by organophosphorus insecticides and nerve agents
-
Albuquerque, X. E., Pereira, E. F. R., Aracava, Y., Fawcett, W. P., Oliveira, M., Randall, W. R., Hamilton, T. A., Kan, R. K., Romano, J. A., Jr., and Adler, M. (2006) Effective countermeasure against poisoning by organophosphorus insecticides and nerve agents, Proc. Natl. Acad. Sci. U.S.A. 103, 13220-13225.
-
(2006)
Proc. Natl. Acad. Sci. U.S.A
, vol.103
, pp. 13220-13225
-
-
Albuquerque, X.E.1
Pereira, E.F.R.2
Aracava, Y.3
Fawcett, W.P.4
Oliveira, M.5
Randall, W.R.6
Hamilton, T.A.7
Kan, R.K.8
Romano Jr., J.A.9
Adler, M.10
-
4
-
-
0026748791
-
Characterization of the zinc binding site of bacterial phosphotriesterase
-
Omburo, G. A., Kuo, J. M., Mullins, L. S., and Raushel, F. M. (1992) Characterization of the zinc binding site of bacterial phosphotriesterase, J. Biol. Chem. 267, 13278-13283.
-
(1992)
J. Biol. Chem
, vol.267
, pp. 13278-13283
-
-
Omburo, G.A.1
Kuo, J.M.2
Mullins, L.S.3
Raushel, F.M.4
-
5
-
-
0026235932
-
Detoxification of organophosphate pesticides using a nylon based immobilized phosphotriesterase from Pseudomonas diminuta
-
Caldwell, S. R., and Raushel, F. M. (1991) Detoxification of organophosphate pesticides using a nylon based immobilized phosphotriesterase from Pseudomonas diminuta, Appl. Biochem. Biotechnol. 31, 59-73.
-
(1991)
Appl. Biochem. Biotechnol
, vol.31
, pp. 59-73
-
-
Caldwell, S.R.1
Raushel, F.M.2
-
6
-
-
0026071672
-
Detoxification of organophosphate pesticides using an immobilized phosphotriesterase from Pseudomonas diminuta
-
Caldwell, S. R., and Raushel, F. M. (2006) Detoxification of organophosphate pesticides using an immobilized phosphotriesterase from Pseudomonas diminuta, Biotechnol. Bioeng. 37, 103-109.
-
(2006)
Biotechnol. Bioeng
, vol.37
, pp. 103-109
-
-
Caldwell, S.R.1
Raushel, F.M.2
-
7
-
-
0642274858
-
Biomaterials for mediation of chemical and biological warfare agents
-
Russell, A. J., Berberich, J. A., Drevon, G. F., and Koepsel, R. R. (2003) Biomaterials for mediation of chemical and biological warfare agents, Annu. Rev. Biomed. Eng. 5, 1-27.
-
(2003)
Annu. Rev. Biomed. Eng
, vol.5
, pp. 1-27
-
-
Russell, A.J.1
Berberich, J.A.2
Drevon, G.F.3
Koepsel, R.R.4
-
8
-
-
0037068856
-
Coordination Geometries of Zn(II) and Cd(II) in Phosphotriesterase: Influence of Water Molecules in the Active Site
-
Krauss, M., Olsen, L., Antony, J., and Hemmingsen, L. (2002) Coordination Geometries of Zn(II) and Cd(II) in Phosphotriesterase: Influence of Water Molecules in the Active Site, J. Phys. Chem. B 106, 9446-9453.
-
(2002)
J. Phys. Chem. B
, vol.106
, pp. 9446-9453
-
-
Krauss, M.1
Olsen, L.2
Antony, J.3
Hemmingsen, L.4
-
9
-
-
0035234441
-
Ab Initio Structure of the Active Site of Phosphotriesterase
-
Krauss, M. (2001) Ab Initio Structure of the Active Site of Phosphotriesterase, J. Chem. Inf. Model. 41, 8-17.
-
(2001)
J. Chem. Inf. Model
, vol.41
, pp. 8-17
-
-
Krauss, M.1
-
10
-
-
0001099193
-
Ab initio determination of the structure of the active site of a metalloenzyme: Metal substitution in phosphotriesterase using density functional methods
-
Kafafi, S. A., and Krauss, M. (1999) Ab initio determination of the structure of the active site of a metalloenzyme: Metal substitution in phosphotriesterase using density functional methods, Int. J. Quantum Chem. 75, 289-299.
-
(1999)
Int. J. Quantum Chem
, vol.75
, pp. 289-299
-
-
Kafafi, S.A.1
Krauss, M.2
-
11
-
-
0035819590
-
-
Koča, J., Zhan, C. G., Rittenhouse, R. C., and Ornstein, R. L. (2001) Mobility of the Active Site Bound Paraoxon and Sarin in Zinc-Phosphotriesterase by Molecular Dynamics Simulation and Quantum Chemical Calculation, J. Am. Chem. Soc. 123, 817-826.
-
Koča, J., Zhan, C. G., Rittenhouse, R. C., and Ornstein, R. L. (2001) Mobility of the Active Site Bound Paraoxon and Sarin in Zinc-Phosphotriesterase by Molecular Dynamics Simulation and Quantum Chemical Calculation, J. Am. Chem. Soc. 123, 817-826.
-
-
-
-
12
-
-
0037328259
-
Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics
-
Koča, J., Zhan, C.-G., Rittenhouse, R. C., and Ornstein, R. L. (2003) Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics, J. Comput. Chem. 24, 368-378.
-
(2003)
J. Comput. Chem
, vol.24
, pp. 368-378
-
-
Koča, J.1
Zhan, C.-G.2
Rittenhouse, R.C.3
Ornstein, R.L.4
-
13
-
-
0033581183
-
-
Zhan, C. G., de Souza, O. N., Rittenhouse, R., and Ornstein, R. L. (1999) Determination of Two Structural Forms of Catalytic Bridging Ligand in Zinc-Phosphotriesterase by Molecular Dynamics Simulation and Quantum Chemical Calculation, J. Am. Chem. Soc. 121, 7279-7282.
-
Zhan, C. G., de Souza, O. N., Rittenhouse, R., and Ornstein, R. L. (1999) Determination of Two Structural Forms of Catalytic Bridging Ligand in Zinc-Phosphotriesterase by Molecular Dynamics Simulation and Quantum Chemical Calculation, J. Am. Chem. Soc. 121, 7279-7282.
-
-
-
-
14
-
-
0037165455
-
Theoretical Determination of Two Structural Forms of the Active Site in Cadmium-Containing Phosphotriesterases
-
Zheng, F., Zhan, C. G., and Ornstein, R. L. (2002) Theoretical Determination of Two Structural Forms of the Active Site in Cadmium-Containing Phosphotriesterases, J. Phys. Chem. B 106, 717-722.
-
(2002)
J. Phys. Chem. B
, vol.106
, pp. 717-722
-
-
Zheng, F.1
Zhan, C.G.2
Ornstein, R.L.3
-
15
-
-
0035543503
-
Theoretical studies of reaction pathways and energy barriers for alkaline hydrolysis of phosphotriesterase substrates paraoxon and related toxic phosphofluoridate nerve agents
-
Zheng, F., Zhan, C.-G., and Ornstein, R. L. (2001) Theoretical studies of reaction pathways and energy barriers for alkaline hydrolysis of phosphotriesterase substrates paraoxon and related toxic phosphofluoridate nerve agents, J. Chem. Soc., Perkin Trans. 2, 2355-2363.
-
(2001)
J. Chem. Soc., Perkin Trans
, vol.2
, pp. 2355-2363
-
-
Zheng, F.1
Zhan, C.-G.2
Ornstein, R.L.3
-
16
-
-
0035889687
-
Successful molecular dynamics simulation of two zinc complexes bridged by a hydroxide in phosphotriesterase using the cationic dummy atom method
-
Pang, Y.-P. (2001) Successful molecular dynamics simulation of two zinc complexes bridged by a hydroxide in phosphotriesterase using the cationic dummy atom method, Proteins: Struct., Funct., Genet. 45, 183-189.
-
(2001)
Proteins: Struct., Funct., Genet
, vol.45
, pp. 183-189
-
-
Pang, Y.-P.1
-
17
-
-
27444433822
-
Ab Initio Molecular Orbital and Density Functional Studies on the Solvolysis of Sarin and O,S-Dimethyl Methylphosphonothiolate, a VX-like Compound
-
Šečkute, J., Menke, J. L., Emnett, R. J., Patterson, E. V., and Cramer, C. J. (2005) Ab Initio Molecular Orbital and Density Functional Studies on the Solvolysis of Sarin and O,S-Dimethyl Methylphosphonothiolate, a VX-like Compound, J. Org. Chem. 70, 8649-8660.
-
(2005)
J. Org. Chem
, vol.70
, pp. 8649-8660
-
-
Šečkute, J.1
Menke, J.L.2
Emnett, R.J.3
Patterson, E.V.4
Cramer, C.J.5
-
18
-
-
2442496666
-
Mechanism for the Hydrolysis of Organophosphates by the Bacterial Phosphotriesterase
-
Aubert, S. D., Li, Y., and Raushel, F. M. (2004) Mechanism for the Hydrolysis of Organophosphates by the Bacterial Phosphotriesterase, Biochemistry 43, 5707-5715.
-
(2004)
Biochemistry
, vol.43
, pp. 5707-5715
-
-
Aubert, S.D.1
Li, Y.2
Raushel, F.M.3
-
19
-
-
33748584863
-
Mechanisms and free energies of enzymatic reactions
-
Gao, J., Ma, S., Major, D. T., Nam, K., Pu, J., and Truhlar, D. G. (2006) Mechanisms and free energies of enzymatic reactions, Chem. Rev. 106, 3188-3209.
-
(2006)
Chem. Rev
, vol.106
, pp. 3188-3209
-
-
Gao, J.1
Ma, S.2
Major, D.T.3
Nam, K.4
Pu, J.5
Truhlar, D.G.6
-
20
-
-
84962367344
-
Methods and applications of combined quantum mechanical and molecular mechanical potentials
-
Gao, J. (1995) Methods and applications of combined quantum mechanical and molecular mechanical potentials, Rev. Comput. Chem. 7, 119-185.
-
(1995)
Rev. Comput. Chem
, vol.7
, pp. 119-185
-
-
Gao, J.1
-
21
-
-
0029993512
-
Three-Dimensional Structure of the Zinc-Containing Phosphotriesterase with the Bound Substrate Analog Diethyl 4-Methylbenzylphosphonate
-
Vanhooke, J. L., Benning, M. M., Raushel, F. M., and Holden, H. M. (1996) Three-Dimensional Structure of the Zinc-Containing Phosphotriesterase with the Bound Substrate Analog Diethyl 4-Methylbenzylphosphonate, Biochemistry 35, 6020-6025.
-
(1996)
Biochemistry
, vol.35
, pp. 6020-6025
-
-
Vanhooke, J.L.1
Benning, M.M.2
Raushel, F.M.3
Holden, H.M.4
-
22
-
-
0034730534
-
The Binding of Substrate Analogs to Phosphotriesterase
-
Benning, M. M., Hong, S.-B., Raushel, F. M., and Holden, H. M. (2000) The Binding of Substrate Analogs to Phosphotriesterase, J. Biol. Chem. 275, 30556-30560.
-
(2000)
J. Biol. Chem
, vol.275
, pp. 30556-30560
-
-
Benning, M.M.1
Hong, S.-B.2
Raushel, F.M.3
Holden, H.M.4
-
23
-
-
0001431264
-
Binuclear metallohydrolases
-
Wilcox, D. E. (1996) Binuclear metallohydrolases, Chem. Rev. 96, 2435-2458.
-
(1996)
Chem. Rev
, vol.96
, pp. 2435-2458
-
-
Wilcox, D.E.1
-
24
-
-
33748502826
-
The catalytic mechanisms of binuclear metallohydrolases
-
Mitić, N., Smith, S. J., Neves, A., Guddat, L. W., Gahan, L. R., and Schenk, G. (2006) The catalytic mechanisms of binuclear metallohydrolases, Chem. Rev. 106, 3338-3363.
-
(2006)
Chem. Rev
, vol.106
, pp. 3338-3363
-
-
Mitić, N.1
Smith, S.J.2
Neves, A.3
Guddat, L.W.4
Gahan, L.R.5
Schenk, G.6
-
25
-
-
0025836538
-
Limits of diffusion in the hydrolysis of substrates by the phosphotriesterase from Pseudomonas diminuta
-
Caldwell, S. R., Newcomb, J. R., Schlecht, K. A., and Raushel, F. M. (1991) Limits of diffusion in the hydrolysis of substrates by the phosphotriesterase from Pseudomonas diminuta, Biochemistry 30, 7438-7444.
-
(1991)
Biochemistry
, vol.30
, pp. 7438-7444
-
-
Caldwell, S.R.1
Newcomb, J.R.2
Schlecht, K.A.3
Raushel, F.M.4
-
26
-
-
33748591572
-
Enzymatic mechanisms of phosphate and sulfate transfer
-
Cleland, W. W., and Hengge, A. C. (2006) Enzymatic mechanisms of phosphate and sulfate transfer, Chem. Rev. 106, 3252-3278.
-
(2006)
Chem. Rev
, vol.106
, pp. 3252-3278
-
-
Cleland, W.W.1
Hengge, A.C.2
-
27
-
-
0033604866
-
Stereochemical Constraints on the Substrate Specificity of Phosphotriesterase
-
Hong, S. B., and Raushel, F. M. (1999) Stereochemical Constraints on the Substrate Specificity of Phosphotriesterase, Biochemistry 38, 1159-1165.
-
(1999)
Biochemistry
, vol.38
, pp. 1159-1165
-
-
Hong, S.B.1
Raushel, F.M.2
-
28
-
-
0035814818
-
Structural Determinants of the Substrate and Stereochemical Specificity of Phosphotriesterase
-
Chen-Goodspeed, M., Sogorb, M. A., Wu, F., Hong, S. B., and Raushel, F. M. (2001) Structural Determinants of the Substrate and Stereochemical Specificity of Phosphotriesterase, Biochemistry 40, 1325-1331.
-
(2001)
Biochemistry
, vol.40
, pp. 1325-1331
-
-
Chen-Goodspeed, M.1
Sogorb, M.A.2
Wu, F.3
Hong, S.B.4
Raushel, F.M.5
-
29
-
-
0024281297
-
Mechanism and stereochemical course at phosphorus of the reaction catalyzed by a bacterial phosphotriesterase
-
Lewis, V. E., Donarski, W. J., Wild, J. R., and Raushel, F. M. (1988) Mechanism and stereochemical course at phosphorus of the reaction catalyzed by a bacterial phosphotriesterase, Biochemistry 27, 1591-1597.
-
(1988)
Biochemistry
, vol.27
, pp. 1591-1597
-
-
Lewis, V.E.1
Donarski, W.J.2
Wild, J.R.3
Raushel, F.M.4
-
30
-
-
4243553426
-
Density-functional exchange-energy approximation with correct asymptotic behavior
-
Becke, A. D. (1988) Density-functional exchange-energy approximation with correct asymptotic behavior, Phys. Rev. A 38, 3098.
-
(1988)
Phys. Rev. A
, vol.38
, pp. 3098
-
-
Becke, A.D.1
-
31
-
-
0345491105
-
Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
-
Lee, C., Yang, W., and Parr, R. G. (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density, Phys. Rev. B 37, 785.
-
(1988)
Phys. Rev. B
, vol.37
, pp. 785
-
-
Lee, C.1
Yang, W.2
Parr, R.G.3
-
32
-
-
33751157732
-
Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force
-
Stephens, P. J., Devlin, F. J., Chabalowski, C. F., and Frisch, M. J. (1994) Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force, J. Phys. Chem. 98, 11623.
-
(1994)
J. Phys. Chem
, vol.98
, pp. 11623
-
-
Stephens, P.J.1
Devlin, F.J.2
Chabalowski, C.F.3
Frisch, M.J.4
-
33
-
-
4243810035
-
Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches
-
Aqvist, J., and Warshel, A. (1993) Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches, Chem. Rev. 93, 2523-2544.
-
(1993)
Chem. Rev
, vol.93
, pp. 2523-2544
-
-
Aqvist, J.1
Warshel, A.2
-
34
-
-
84986513644
-
A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations
-
Field, M. J., Bash, P. A., and Karplus, M. (1990) A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations, J. Comput. Chem. 11, 700-733.
-
(1990)
J. Comput. Chem
, vol.11
, pp. 700-733
-
-
Field, M.J.1
Bash, P.A.2
Karplus, M.3
-
35
-
-
0027125907
-
A prior evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations
-
Gao, J., and Xia, X. (1992) A prior evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations, Science 258, 631-635.
-
(1992)
Science
, vol.258
, pp. 631-635
-
-
Gao, J.1
Xia, X.2
-
36
-
-
0035786390
-
The QM/MM approach to enzymatic reactions
-
Mulholland, A. J. (2001) The QM/MM approach to enzymatic reactions, Theor. Comput. Chem. 9, 597-653.
-
(2001)
Theor. Comput. Chem
, vol.9
, pp. 597-653
-
-
Mulholland, A.J.1
-
37
-
-
0346726109
-
How enzymes work: Analysis by modern rate theory and computer simulations
-
Garcia-Viloca, M., Gao, J., Karplus, M., and Truhlar, D. G. (2004) How enzymes work: Analysis by modern rate theory and computer simulations, Science 303, 186-195.
-
(2004)
Science
, vol.303
, pp. 186-195
-
-
Garcia-Viloca, M.1
Gao, J.2
Karplus, M.3
Truhlar, D.G.4
-
38
-
-
0036025446
-
Quantum mechanical methods for enzyme kinetics
-
Gao, J., and Truhlar, D. G. (2002) Quantum mechanical methods for enzyme kinetics, Annu. Rev. Phys. Chem. 53, 467-505.
-
(2002)
Annu. Rev. Phys. Chem
, vol.53
, pp. 467-505
-
-
Gao, J.1
Truhlar, D.G.2
-
39
-
-
0000078321
-
Potential of mean force for the isomerization of DMF in aqueous solution: A Monte Carlo QM/MM simulation study
-
Gao, J. (1993) Potential of mean force for the isomerization of DMF in aqueous solution: a Monte Carlo QM/MM simulation study, J. Am. Chem. Soc. 115, 2930-2935.
-
(1993)
J. Am. Chem. Soc
, vol.115
, pp. 2930-2935
-
-
Gao, J.1
-
40
-
-
0028408529
-
Origin of the solvent effects on the barrier to amide isomerization from combined QM/MM Monte Carlo simulations
-
Gao, J. (1994) Origin of the solvent effects on the barrier to amide isomerization from combined QM/MM Monte Carlo simulations, Proc. - Indian Acad. Sci., Chem. Sci. 106, 507-519.
-
(1994)
Proc. - Indian Acad. Sci., Chem. Sci
, vol.106
, pp. 507-519
-
-
Gao, J.1
-
41
-
-
0034798239
-
New Insight on the Origin of the Unusual Acidity of Meldrum's Acid from ab Initio and Combined QM/MM Simulation Study
-
Byun, K., Mo, Y., and Gao, J. (2001) New Insight on the Origin of the Unusual Acidity of Meldrum's Acid from ab Initio and Combined QM/MM Simulation Study, J. Am. Chem. Soc. 123, 3974-3979.
-
(2001)
J. Am. Chem. Soc
, vol.123
, pp. 3974-3979
-
-
Byun, K.1
Mo, Y.2
Gao, J.3
-
42
-
-
0842341771
-
AM1: A new general purpose quantum mechanical molecular model
-
Dewar, M. J. S., Zoebisch, E. G., Healy, E. F., and Stewart, J. P. (1985) AM1: A new general purpose quantum mechanical molecular model, J. Am. Chem. Soc. 107, 3902-3909.
-
(1985)
J. Am. Chem. Soc. 107
, pp. 3902-3909
-
-
Dewar, M.J.S.1
Zoebisch, E.G.2
Healy, E.F.3
Stewart, J.P.4
-
43
-
-
33845280036
-
AM1 parameters for zinc
-
Dewar, M. J. S., and Merz, K. M., Jr. (1988) AM1 parameters for zinc, Organometallics 7, 522-524.
-
(1988)
Organometallics
, vol.7
, pp. 522-524
-
-
Dewar, M.J.S.1
Merz Jr., K.M.2
-
44
-
-
0011123246
-
AM1 parameters for phosphorus
-
Dewar, M. J. S., and Jie, C. (1989) AM1 parameters for phosphorus, THEOCHEM 187, 1-13.
-
(1989)
THEOCHEM 187
, pp. 1-13
-
-
Dewar, M.J.S.1
Jie, C.2
-
45
-
-
0000411659
-
A Generalized Hybrid Orbital (GHO) Method for the Treatment of Boundary Atoms in Combined QM/MM Calculations
-
Gao, J., Amara, P., Alhambra, C., and Field, M. J. (1998) A Generalized Hybrid Orbital (GHO) Method for the Treatment of Boundary Atoms in Combined QM/MM Calculations, J. Phys. Chem. A 102, 4714-4721.
-
(1998)
J. Phys. Chem. A
, vol.102
, pp. 4714-4721
-
-
Gao, J.1
Amara, P.2
Alhambra, C.3
Field, M.J.4
-
46
-
-
0034375393
-
The generalized hybrid orbital method for combined quantum mechanical/molecular mechanical calculations: Formulation and tests of the analytical derivatives
-
Amara, P., Field, M. J., Alhambra, C., and Gao, J. (2000) The generalized hybrid orbital method for combined quantum mechanical/molecular mechanical calculations: formulation and tests of the analytical derivatives, Theor. Chem. Acc. 104, 336-343.
-
(2000)
Theor. Chem. Acc
, vol.104
, pp. 336-343
-
-
Amara, P.1
Field, M.J.2
Alhambra, C.3
Gao, J.4
-
47
-
-
0041784950
-
-
MacKerell, A. D., Jr., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T. K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher, W. E., III, Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D., and Karplus, M. (1998) All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins, J. Phys. Chem. B 102, 3586-3616.
-
MacKerell, A. D., Jr., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T. K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher, W. E., III, Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D., and Karplus, M. (1998) All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins, J. Phys. Chem. B 102, 3586-3616.
-
-
-
-
48
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., and Klein, M. L. (1983) Comparison of simple potential functions for simulating liquid water, J. Chem. Phys. 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
-
49
-
-
84873055189
-
-
Wiley, New York
-
Hehre, W. J., Radom, L., Schleyer, P. v. R., and Pople, J. A. (1986) Ab initio molecular orbital theory, Wiley, New York.
-
(1986)
Ab initio molecular orbital theory
-
-
Hehre, W.J.1
Radom, L.2
Schleyer, P.V.R.3
Pople, J.A.4
-
50
-
-
0003569570
-
-
Oxford University Press, Clarendon Press, New York, NY, Oxford, U.K
-
Parr, R. G., and Yang, W. (1989) Density-functional theory of atoms and molecules, Oxford University Press, Clarendon Press, New York, NY, Oxford, U.K.
-
(1989)
Density-functional theory of atoms and molecules
-
-
Parr, R.G.1
Yang, W.2
-
51
-
-
21244497608
-
Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis
-
Friesner, R. A., and Guallar, V. (2005) Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis, Annu. Rev. Phys. Chem. 56, 389-427.
-
(2005)
Annu. Rev. Phys. Chem
, vol.56
, pp. 389-427
-
-
Friesner, R.A.1
Guallar, V.2
-
52
-
-
0035785737
-
Simulations of enzymatic systems: Perspectives from Car-Parrinello molecular dynamics simulations
-
Carloni, P., and Rothlisberger, U. (2001) Simulations of enzymatic systems: Perspectives from Car-Parrinello molecular dynamics simulations, Theor. Comput. Chem. 9, 215-251.
-
(2001)
Theor. Comput. Chem
, vol.9
, pp. 215-251
-
-
Carloni, P.1
Rothlisberger, U.2
-
53
-
-
0025390935
-
MOPAC: A semiempirical molecular orbital program
-
Stewart, J. J. P. (1990) MOPAC: a semiempirical molecular orbital program, J. Comput.-Aided Mol. Des. 4, 1-105.
-
(1990)
J. Comput.-Aided Mol. Des
, vol.4
, pp. 1-105
-
-
Stewart, J.J.P.1
-
54
-
-
0035138648
-
-
Cui, Q., Elstner, M., Kaxiras, E., Frauenheim, T., and Karplus, M. (2001) J. Phys. Chem. B 105, 569.
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 569
-
-
Cui, Q.1
Elstner, M.2
Kaxiras, E.3
Frauenheim, T.4
Karplus, M.5
-
55
-
-
29244444539
-
Potential of Mean Force Calculation for the Proton and Hydride Transfer Reactions Catalyzed by Medium-Chain Acyl-CoA Dehydrogenase: Effect of Mutations on Enzyme Catalysis
-
Bhattacharyya, S., Ma, S., Stankovich, M. T., Truhlar, D. G., and Gao, J. (2005) Potential of Mean Force Calculation for the Proton and Hydride Transfer Reactions Catalyzed by Medium-Chain Acyl-CoA Dehydrogenase: Effect of Mutations on Enzyme Catalysis, Biochemistry 44, 16549-16562.
-
(2005)
Biochemistry
, vol.44
, pp. 16549-16562
-
-
Bhattacharyya, S.1
Ma, S.2
Stankovich, M.T.3
Truhlar, D.G.4
Gao, J.5
-
56
-
-
5444222194
-
PM3-compatible zinc parameters optimized for metalloenzyme active sites
-
Brothers, E. N., Suarez, D., Deerfield, D. W., II, and Merz, K. M., Jr. (2004) PM3-compatible zinc parameters optimized for metalloenzyme active sites, J. Comput. Chem. 25, 1677-1692.
-
(2004)
J. Comput. Chem
, vol.25
, pp. 1677-1692
-
-
Brothers, E.N.1
Suarez, D.2
Deerfield II, D.W.3
Merz Jr., K.M.4
-
57
-
-
34547625687
-
A specific reaction parameterization of the AM1/d Hamiltonian for phosphoryl transfer reactions
-
(a) Nam, K., Cui, Q., Gao, J., and York, D. M. (2007) A specific reaction parameterization of the AM1/d Hamiltonian for phosphoryl transfer reactions, J. Chem. Theory Comput. 3, 486-504.
-
(2007)
J. Chem. Theory Comput
, vol.3
, pp. 486-504
-
-
Nam, K.1
Cui, Q.2
Gao, J.3
York, D.M.4
-
58
-
-
0037718593
-
Parameterization of semiempirical methods to treat nucleophilic attacks to biological phosphates: AM1/d parameters for phosphorus
-
(b) Lopez, X., and York, D. M. (2003) Parameterization of semiempirical methods to treat nucleophilic attacks to biological phosphates: AM1/d parameters for phosphorus, Theor. Chem. Acc. 109, 149-159.
-
(2003)
Theor. Chem. Acc
, vol.109
, pp. 149-159
-
-
Lopez, X.1
York, D.M.2
-
59
-
-
0347174862
-
Dual-level methods for electronic structure calculations of potential energy functions that use quantum mechanics as the lower level
-
Gao, J, and Thompson, M. A, Eds, pp, American Chemical Society, Wahsington, DC
-
Corchado, J. C., and Truhlar, D. G. (1998) Dual-level methods for electronic structure calculations of potential energy functions that use quantum mechanics as the lower level, in Combined Quantum Mechanical and Molecular Mechanical Methods (Gao, J., and Thompson, M. A., Eds.) pp 106-127, American Chemical Society, Wahsington, DC.
-
(1998)
Combined Quantum Mechanical and Molecular Mechanical Methods
, pp. 106-127
-
-
Corchado, J.C.1
Truhlar, D.G.2
-
60
-
-
0000556829
-
A Hybrid-Potential Free-Energy Study of the Isomerization Step of the Acetohydroxy Acid Isomeroreductase Reaction
-
Proust-De Martin, F., Dumas, R., and Field, M. J. (2000) A Hybrid-Potential Free-Energy Study of the Isomerization Step of the Acetohydroxy Acid Isomeroreductase Reaction, J. Am. Chem. Soc. 122, 7688-7697.
-
(2000)
J. Am. Chem. Soc
, vol.122
, pp. 7688-7697
-
-
Proust-De Martin, F.1
Dumas, R.2
Field, M.J.3
-
61
-
-
15544388511
-
Computing Kinetic Isotope Effects for Chorismate Mutase with High Accuracy. A New DFT/MM Strategy
-
Marti, S., Moliner, V., Tunon, I., and Williams, I. H. (2005) Computing Kinetic Isotope Effects for Chorismate Mutase with High Accuracy. A New DFT/MM Strategy, J. Phys. Chem. B 109, 3707-3710.
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 3707-3710
-
-
Marti, S.1
Moliner, V.2
Tunon, I.3
Williams, I.H.4
-
62
-
-
33845926809
-
Improving the QM/MM Description of Chemical Processes: A Dual Level Strategy To Explore the Potential Energy Surface in Very Large Systems
-
Marti, S., Moliner, V., and Tunon, I. (2005) Improving the QM/MM Description of Chemical Processes: A Dual Level Strategy To Explore the Potential Energy Surface in Very Large Systems, J. Chem. Theory Comput. 1, 1008-1016.
-
(2005)
J. Chem. Theory Comput
, vol.1
, pp. 1008-1016
-
-
Marti, S.1
Moliner, V.2
Tunon, I.3
-
63
-
-
29644433206
-
A QM/MM Exploration of the Potential Energy Surface of Pyruvate to Lactate Transformation Catalyzed by LDH. Improving the Accuracy of Semiempirical Descriptions
-
Ferrer, S., Ruiz-Pernia, J. J., Tunon, I., Moliner, V., Garcia-Viloca, M., Gonzalez-Lafont, A., and Lluch, J. M. (2005) A QM/MM Exploration of the Potential Energy Surface of Pyruvate to Lactate Transformation Catalyzed by LDH. Improving the Accuracy of Semiempirical Descriptions, J. Chem. Theory Comput. 1, 750-761.
-
(2005)
J. Chem. Theory Comput
, vol.1
, pp. 750-761
-
-
Ferrer, S.1
Ruiz-Pernia, J.J.2
Tunon, I.3
Moliner, V.4
Garcia-Viloca, M.5
Gonzalez-Lafont, A.6
Lluch, J.M.7
-
64
-
-
33646508010
-
Accurate QM/MM Free Energy Calculations of Enzyme Reactions: Methylation by Catechol O-Methyltransferase
-
Rod, T. H., and Ryde, U. (2005) Accurate QM/MM Free Energy Calculations of Enzyme Reactions: Methylation by Catechol O-Methyltransferase, J. Chem. Theory Comput. 1, 1240-1251.
-
(2005)
J. Chem. Theory Comput
, vol.1
, pp. 1240-1251
-
-
Rod, T.H.1
Ryde, U.2
-
65
-
-
31144441067
-
ONIOM: A Multi-Layered Integrated MO + MM Method for Geometry Optimizations and Single Point Energy Predictions. A Test for Diels-Alder Reactions and Pt(P(t-Bu)3)2 + H2 Oxidative Addition
-
Svensson, M., Humbel, S., Froese, R. D. J., Matsubara, T., Sieber, S., and Morokuma, K. (1996) ONIOM: A Multi-Layered Integrated MO + MM Method for Geometry Optimizations and Single Point Energy Predictions. A Test for Diels-Alder Reactions and Pt(P(t-Bu)3)2 + H2 Oxidative Addition, J. Phys. Chem. 100, 19357-19363.
-
(1996)
J. Phys. Chem
, vol.100
, pp. 19357-19363
-
-
Svensson, M.1
Humbel, S.2
Froese, R.D.J.3
Matsubara, T.4
Sieber, S.5
Morokuma, K.6
-
66
-
-
0345713551
-
Hybrid Models for Combined Quantum Mechanical and Molecular Mechanical Approaches
-
Bakowies, D., and Thiel, W. (1996) Hybrid Models for Combined Quantum Mechanical and Molecular Mechanical Approaches, J. Phys. Chem. 100, 10580-10594.
-
(1996)
J. Phys. Chem
, vol.100
, pp. 10580-10594
-
-
Bakowies, D.1
Thiel, W.2
-
67
-
-
0037459224
-
Importance of substrate and cofactor polarization in the active site of dihydrofolate reductase
-
Garcia-Viloca, M., Truhlar Donald, G., and Gao, J. (2003) Importance of substrate and cofactor polarization in the active site of dihydrofolate reductase, J. Mol. Biol. 327, 549-560.
-
(2003)
J. Mol. Biol
, vol.327
, pp. 549-560
-
-
Garcia-Viloca, M.1
Truhlar Donald, G.2
Gao, J.3
-
68
-
-
84962407457
-
-
Orozco, M., Luque, F. J., Habibollahzadeh, D., and Gao, J. (1995) The polarization contribution to the free energy of hydration, J. Chem. Phys. 102, 6145-6152. Erratum, J. Chem. Phys. 103, 9112.
-
Orozco, M., Luque, F. J., Habibollahzadeh, D., and Gao, J. (1995) The polarization contribution to the free energy of hydration, J. Chem. Phys. 102, 6145-6152. Erratum, J. Chem. Phys. 103, 9112.
-
-
-
-
69
-
-
0001491955
-
Hybrid Quantum Mechanical/Molecular Mechanical Simulations: An Alternative Avenue to Solvent Effects in Organic Chemistry
-
Gao, J. (1996) Hybrid Quantum Mechanical/Molecular Mechanical Simulations: An Alternative Avenue to Solvent Effects in Organic Chemistry, Acc. Chem. Res. 29, 298-305.
-
(1996)
Acc. Chem. Res
, vol.29
, pp. 298-305
-
-
Gao, J.1
-
70
-
-
5244287607
-
An Automated Procedure for Simulating Chemical Reactions in Solution. Application to the Decarboxylation of 3-Carboxybenzisoxazole in Water
-
Gao, J. (1995) An Automated Procedure for Simulating Chemical Reactions in Solution. Application to the Decarboxylation of 3-Carboxybenzisoxazole in Water, J. Am. Chem. Soc. 117, 8600-8607.
-
(1995)
J. Am. Chem. Soc
, vol.117
, pp. 8600-8607
-
-
Gao, J.1
-
71
-
-
0000342940
-
Ab initio QM/MM simulations with a molecular orbital-valence bond (MOVB) method: Application to an SN2 reaction in water
-
Mo, Y., and Gao, J. (2000) Ab initio QM/MM simulations with a molecular orbital-valence bond (MOVB) method: application to an SN2 reaction in water, J. Comput. Chem. 21, 1458-1469.
-
(2000)
J. Comput. Chem
, vol.21
, pp. 1458-1469
-
-
Mo, Y.1
Gao, J.2
-
72
-
-
0031490976
-
Solvent effects on the n → π* transition of pyrimidine in aqueous solution
-
Gao, J., and Byun, K. (1997) Solvent effects on the n → π* transition of pyrimidine in aqueous solution, Theor. Chem. Acc. 96, 151-156.
-
(1997)
Theor. Chem. Acc
, vol.96
, pp. 151-156
-
-
Gao, J.1
Byun, K.2
-
73
-
-
0000188281
-
The MIDI! basis set for quantum mechanical calculations of molecular geometries and partial charges
-
Easton, R. E., Giesen, D. J., Welch, A., Cramer, C. J., and Truhlar, D. G. (1996) The MIDI! basis set for quantum mechanical calculations of molecular geometries and partial charges, Theor. Chim. Acta 93, 281-301.
-
(1996)
Theor. Chim. Acta
, vol.93
, pp. 281-301
-
-
Easton, R.E.1
Giesen, D.J.2
Welch, A.3
Cramer, C.J.4
Truhlar, D.G.5
-
74
-
-
36249029970
-
-
Frisch, M. J, Trucks, G. W, Schlegel, H. B, Scuseria, G. E, Robb, M. A, Cheeseman, J. R, Montgomery, J. A, Jr, Vreven, T, Kudin, K. N, Burant, J. C, Millam, J. M, Iyengar, S. S, Tomasi, J, Barone, V, Mennucci, B, Cossi, M, Scalmani, G, Rega, N, Petersson, G. A, Nakatsuji, H, Hada, M, Ehara, M, Toyota, K, Fukuda, R, Hasegawa, J, Ishida, M, Nakajima, T, Honda, Y, Kitao, O, Nakai, H, Klene, M, Li, X, Knox, J. E, Hratchian, H. P, Cross, J. B, Bakken, V, Adamo, C, Jaramillo, J, Gomperts, R, Stratmann, R. E, Yazyev, O, Austin, A. J, Cammi, R, Pomelli, C, Ochterski, J. W, Ayala, P. Y, Morokuma, K, Voth, G. A, Salvador, P, Dannenberg, J. J, Zakrzewski, V. G, Dapprich, S, Daniels, A. D, Strain, M. C, Farkas, O, Malick, D. K, Rabuck, A. D, Raghavachari, K, Foresman, J. B, Ortiz, J. V, Cui, Q, Baboul, A. G, Clifford, S, Cioslowski, J, Stefanov, B. B, Liu, G, Liashenko, A, Piskorz, P, Komaromi, I, Martin, R. L, Fox, D. J, Keit
-
Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Montgomery, J. A., Jr., Vreven, T., Kudin, K. N., Burant, J. C., Millam, J. M., Iyengar, S. S., Tomasi, J., Barone, V., Mennucci, B., Cossi, M., Scalmani, G., Rega, N., Petersson, G. A., Nakatsuji, H., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Klene, M., Li, X., Knox, J. E., Hratchian, H. P., Cross, J. B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R. E., Yazyev, O., Austin, A. J., Cammi, R., Pomelli, C., Ochterski, J. W., Ayala, P. Y., Morokuma, K., Voth, G. A., Salvador, P., Dannenberg, J. J., Zakrzewski, V. G., Dapprich, S., Daniels, A. D., Strain, M. C., Farkas, O., Malick, D. K., Rabuck, A. D., Raghavachari, K., Foresman, J. B., Ortiz, J. V., Cui, Q., Baboul, A. G., Clifford, S., Cioslowski, J., Stefanov, B. B., Liu, G., Liashenko, A., Piskorz, P., Komaromi, I., Martin, R. L., Fox, D. J., Keith, T., Al-Laham, M. A., Peng, C. Y., Nanayakkara, A., Challacombe, M., Gill, P. M. W., Johnson, B., Chen, W., Wong, M. W., Gonzalez, C., and Pople, J. A. (2004) Gaussian 03, revision C.02, Gaussian, Inc., Wallingford, CT.
-
-
-
-
75
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., and Karplus, M. (1983) CHARMM: a program for macromolecular energy, minimization, and dynamics calculations, J. Comput. Chem. 4, 187-217.
-
(1983)
J. Comput. Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
77
-
-
33646471468
-
Statistical mechanics of fluid mixtures
-
Kirkwood, J. G. (1935) Statistical mechanics of fluid mixtures, J. Chem. Phys. 3, 300-313.
-
(1935)
J. Chem. Phys
, vol.3
, pp. 300-313
-
-
Kirkwood, J.G.1
-
78
-
-
0035940264
-
Energetics and dynamics of enzymatic reactions
-
Villa, J., and Warshel, A. (2001) Energetics and dynamics of enzymatic reactions, J. Phys. Chem. B 105, 7887-7907.
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 7887-7907
-
-
Villa, J.1
Warshel, A.2
-
79
-
-
0342929614
-
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
-
Torrie, G. M., and Valleau, J. P. (1977) Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling, J. Comput. Phys. 23, 187-199.
-
(1977)
J. Comput. Phys
, vol.23
, pp. 187-199
-
-
Torrie, G.M.1
Valleau, J.P.2
-
80
-
-
84986519238
-
The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method
-
Kumar, S., Bouzida, D., Swendsen, R. H., Kollman, P. A., and Rosenberg, J. M. (1992) The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method, J. Comput. Chem. 13, 1011-1021.
-
(1992)
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
-
81
-
-
0035892157
-
Canonical Variational Theory for Enzyme Kinetics with the Protein Mean Force and Multidimensional Quantum Mechanical Tunneling Dynamics. Theory and Application to Liver Alcohol Dehydrogenase
-
Alhambra, C., Corchado, J., Sanchez, M. L., Garcia-Viloca, M., Gao, J., and Truhlar, D. G. (2001) Canonical Variational Theory for Enzyme Kinetics with the Protein Mean Force and Multidimensional Quantum Mechanical Tunneling Dynamics. Theory and Application to Liver Alcohol Dehydrogenase, J. Phys. Chem. B 105, 11326-11340.
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 11326-11340
-
-
Alhambra, C.1
Corchado, J.2
Sanchez, M.L.3
Garcia-Viloca, M.4
Gao, J.5
Truhlar, D.G.6
-
82
-
-
0022068152
-
Active site dynamics in protein molecules: A stochastic boundary molecular-dynamics approach
-
Brooks, C. L., III, Brunger, A., and Karplus, M. (1985) Active site dynamics in protein molecules: a stochastic boundary molecular-dynamics approach, Biopolymers 24, 843-865.
-
(1985)
Biopolymers
, vol.24
, pp. 843-865
-
-
Brooks III, C.L.1
Brunger, A.2
Karplus, M.3
-
83
-
-
0024354001
-
Solvent effects on protein motion and protein effects on solvent motion. Dynamics of the active site region of lysozyme
-
Brooks, C. L., III., and Karplus, M. (1989) Solvent effects on protein motion and protein effects on solvent motion. Dynamics of the active site region of lysozyme, J. Mol. Biol. 208, 159-181.
-
(1989)
J. Mol. Biol
, vol.208
, pp. 159-181
-
-
Brooks III, C.L.1
Karplus, M.2
-
84
-
-
36749119973
-
Deformable stochastic boundaries in molecular dynamics
-
Brooks, C. L., III, and Karplus, M. (1983) Deformable stochastic boundaries in molecular dynamics, J. Chem. Phys. 79, 6312-6325.
-
(1983)
J. Chem. Phys
, vol.79
, pp. 6312-6325
-
-
Brooks III, C.L.1
Karplus, M.2
-
85
-
-
33646940952
-
Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert, J. P., Ciccotti, G., and Berendsen, H. J. C. (1977) Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes, J. Comput. Phys. 23, 327-341.
-
(1977)
J. Comput. Phys
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
86
-
-
22944467757
-
Computer "experiments" on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules
-
Verlet, L. (1967) Computer "experiments" on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules, Phys. Rev. 159, 98-103.
-
(1967)
Phys. Rev
, vol.159
, pp. 98-103
-
-
Verlet, L.1
-
87
-
-
0000846380
-
Hydrogen-bonding interactions in the active site of a low molecular weight protein-tyrosine phosphatase
-
Alhambra, C., and Gao, J. (2000) Hydrogen-bonding interactions in the active site of a low molecular weight protein-tyrosine phosphatase, J. Comput. Chem. 21, 1192-1203.
-
(2000)
J. Comput. Chem
, vol.21
, pp. 1192-1203
-
-
Alhambra, C.1
Gao, J.2
-
89
-
-
0037472678
-
Hydride transfer catalyzed by xylose isomerase: Mechanism and quantum effects
-
Garcia-Viloca, M., Alhambra, C., Truhlar Donald, G., and Gao, J. (2003) Hydride transfer catalyzed by xylose isomerase: mechanism and quantum effects, J. Comput. Chem. 24, 177-190.
-
(2003)
J. Comput. Chem
, vol.24
, pp. 177-190
-
-
Garcia-Viloca, M.1
Alhambra, C.2
Truhlar Donald, G.3
Gao, J.4
-
90
-
-
0029878720
-
VMD: Visual molecular dynamics
-
Humphrey, W., Dalke, A., and Schulten, K. (1996) VMD: visual molecular dynamics, J. Mol. Graphics 14, 33-38.
-
(1996)
J. Mol. Graphics 14
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
91
-
-
36248976080
-
-
Dennington, R, II, Keith, T, Millam, J, Eppinnett, K, Hovell, W. L, and Gilliland, R, 2003 GaussView, version 3.07, Semichem, Inc, Shawnee Mission, KS
-
Dennington, R., II, Keith, T., Millam, J., Eppinnett, K., Hovell, W. L., and Gilliland, R. (2003) GaussView, version 3.07, Semichem, Inc., Shawnee Mission, KS.
-
-
-
-
92
-
-
5244245983
-
A correlation of reaction rates
-
Hammond, G. S. (1955) A correlation of reaction rates, J. Am. Chem. Soc. 77, 334-338.
-
(1955)
J. Am. Chem. Soc
, vol.77
, pp. 334-338
-
-
Hammond, G.S.1
-
93
-
-
0012154673
-
Gaussian-3 (G3) theory for molecules containing first and second-row atoms
-
Curtiss, L. A., Raghavachari, K., Redfern, P. C., Rassolov, V., and Pople, J. A. (1998) Gaussian-3 (G3) theory for molecules containing first and second-row atoms, J. Chem. Phys. 109, 7764-7776.
-
(1998)
J. Chem. Phys
, vol.109
, pp. 7764-7776
-
-
Curtiss, L.A.1
Raghavachari, K.2
Redfern, P.C.3
Rassolov, V.4
Pople, J.A.5
-
94
-
-
36449005292
-
A study of some organic reactions using density functional theory
-
Baker, J., Muir, M., and Andzelm, J. (1995) A study of some organic reactions using density functional theory, J. Chem. Phys. 102, 2063-2079.
-
(1995)
J. Chem. Phys
, vol.102
, pp. 2063-2079
-
-
Baker, J.1
Muir, M.2
Andzelm, J.3
-
95
-
-
0035810443
-
How Well Can Hybrid Density Functional Methods Predict Transition State Geometries and Barrier Heights?
-
Lynch, B. J., and Truhlar, D. G. (2001) How Well Can Hybrid Density Functional Methods Predict Transition State Geometries and Barrier Heights?, J. Phys. Chem. A 105, 2936-2941.
-
(2001)
J. Phys. Chem. A
, vol.105
, pp. 2936-2941
-
-
Lynch, B.J.1
Truhlar, D.G.2
-
96
-
-
0035912842
-
Molecular structure of dihydroorotase: A paradigm for catalysis through the use of a binuclear metal center
-
Thoden, J. B., Phillips, G. N., Jr., Neal, T. M., Raushel, F. M., and Holden, H. M. (2001) Molecular structure of dihydroorotase: a paradigm for catalysis through the use of a binuclear metal center, Biochemistry 40, 6989-6997.
-
(2001)
Biochemistry
, vol.40
, pp. 6989-6997
-
-
Thoden, J.B.1
Phillips Jr., G.N.2
Neal, T.M.3
Raushel, F.M.4
Holden, H.M.5
-
97
-
-
0028225131
-
X-ray Crystallographic Structures of D-Xylose Isomerase-Substrate Complexes Position the Substrate and Provide Evidence for Metal Movement during Catalysis
-
Lavie, A., Allen, K. N., Petsko, G. A., and Ringe, D. (1994) X-ray Crystallographic Structures of D-Xylose Isomerase-Substrate Complexes Position the Substrate and Provide Evidence for Metal Movement during Catalysis, Biochemistry 33, 5469-5480.
-
(1994)
Biochemistry
, vol.33
, pp. 5469-5480
-
-
Lavie, A.1
Allen, K.N.2
Petsko, G.A.3
Ringe, D.4
-
98
-
-
0028953745
-
Design, Synthesis, and Characterization of a Potent Xylose Isomerase Inhibitor, D-Threonohydroxamic Acid, and High-Resolution X-ray Crystallographic Structure of the Enzyme-Inhibitor Complex
-
Allen, K. N., Lavie, A., Petsko, G. A., and Ringe, D. (1995) Design, Synthesis, and Characterization of a Potent Xylose Isomerase Inhibitor, D-Threonohydroxamic Acid, and High-Resolution X-ray Crystallographic Structure of the Enzyme-Inhibitor Complex, Biochemistry 34, 3742-3749.
-
(1995)
Biochemistry
, vol.34
, pp. 3742-3749
-
-
Allen, K.N.1
Lavie, A.2
Petsko, G.A.3
Ringe, D.4
-
99
-
-
33847410577
-
Theoretical Study of the Phosphotriesterase Reaction Mechanism
-
Chen, S.-L., Fang, W.-H., Himo, F. (2007) Theoretical Study of the Phosphotriesterase Reaction Mechanism, J. Phys. Chem. B 111, 1253.
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 1253
-
-
Chen, S.-L.1
Fang, W.-H.2
Himo, F.3
-
100
-
-
0344391945
-
Reaction-Path Energetics and Kinetics of the Hydride Transfer Reaction Catalyzed by Dihydrofolate Reductase
-
Garcia-Viloca, M., Truhlar, D. G., and Gao, J. (2003) Reaction-Path Energetics and Kinetics of the Hydride Transfer Reaction Catalyzed by Dihydrofolate Reductase, Biochemistry 42, 13558-13575.
-
(2003)
Biochemistry
, vol.42
, pp. 13558-13575
-
-
Garcia-Viloca, M.1
Truhlar, D.G.2
Gao, J.3
-
101
-
-
33845377773
-
Energy profile for a nonconcerted SN2 reaction in solution
-
Chandrasekhar, J., and Jorgensen, W. L. (1985) Energy profile for a nonconcerted SN2 reaction in solution, J. Am. Chem. Soc. 107, 2974-2975.
-
(1985)
J. Am. Chem. Soc
, vol.107
, pp. 2974-2975
-
-
Chandrasekhar, J.1
Jorgensen, W.L.2
-
102
-
-
33747503207
-
Transesterification Thio Effects of Phosphate Diesters: Free Energy Barriers and Kinetic and Equilibrium Isotope Effects from Density-Functional Theory
-
Liu, Y., Gregersen, B. A., Hengge, A., and York, D. M. (2006) Transesterification Thio Effects of Phosphate Diesters: Free Energy Barriers and Kinetic and Equilibrium Isotope Effects from Density-Functional Theory, Biochemistry 45, 10043-10053.
-
(2006)
Biochemistry
, vol.45
, pp. 10043-10053
-
-
Liu, Y.1
Gregersen, B.A.2
Hengge, A.3
York, D.M.4
-
104
-
-
23944485399
-
The Structure of an Enzyme-Product Complex Reveals the Critical Role of a Terminal Hydroxide Nucleophile in the Bacterial Phosphotriesterase Mechanism
-
Jackson, C., Kim, H. K., Carr, P. D., Liu, J. W., and Ollis, D. L. (2005) The Structure of an Enzyme-Product Complex Reveals the Critical Role of a Terminal Hydroxide Nucleophile in the Bacterial Phosphotriesterase Mechanism, Biochim. Biophys. Acta 1752, 56.
-
(2005)
Biochim. Biophys. Acta
, vol.1752
, pp. 56
-
-
Jackson, C.1
Kim, H.K.2
Carr, P.D.3
Liu, J.W.4
Ollis, D.L.5
-
105
-
-
0033081891
-
A New Proposal for Urease Mechanism Based on the Crystal Structures of the Native and Inhibited Enzyme From Bacillus Pasteurii: Why Urea hydrolysis Costs two Nickels
-
Benini, S., Rypniewski, W. R., Wilson, K. S., Ciurli, S., and Mangani, S. (1999) A New Proposal for Urease Mechanism Based on the Crystal Structures of the Native and Inhibited Enzyme From Bacillus Pasteurii: Why Urea hydrolysis Costs two Nickels, Struct. Fold. Des. 7, 205.
-
(1999)
Struct. Fold. Des
, vol.7
, pp. 205
-
-
Benini, S.1
Rypniewski, W.R.2
Wilson, K.S.3
Ciurli, S.4
Mangani, S.5
-
106
-
-
0038671973
-
High Resolution X-ray Structure of Isoaspartyl Dipeptidase from Escherichia Coli
-
Thoden, J. B., Marti-Arbona, R., Raushel, F. M., and Holden, H. M. (2003) High Resolution X-ray Structure of Isoaspartyl Dipeptidase from Escherichia Coli, Biochemistry 42, 4874.
-
(2003)
Biochemistry
, vol.42
, pp. 4874
-
-
Thoden, J.B.1
Marti-Arbona, R.2
Raushel, F.M.3
Holden, H.M.4
-
107
-
-
0025974544
-
A Metal-Mediated Hydride Shift Mechanism for Xylose Isomerase based on the 1.6 A Streptomyces Rubiginosus Structure with Xylitol and D-Xylose
-
Whiltlow, M., Howard, A. J., Finzel, B. C., Poulos, T. L., Winborne, E., and Gilliland, G. L. (1991) A Metal-Mediated Hydride Shift Mechanism for Xylose Isomerase based on the 1.6 A Streptomyces Rubiginosus Structure with Xylitol and D-Xylose, Proteins: Struct., Funct., Genet. 9, 153-173.
-
(1991)
Proteins: Struct., Funct., Genet
, vol.9
, pp. 153-173
-
-
Whiltlow, M.1
Howard, A.J.2
Finzel, B.C.3
Poulos, T.L.4
Winborne, E.5
Gilliland, G.L.6
-
108
-
-
24644514643
-
Catalysis by Enzyme Conformational Change
-
Gao, J., Byun, K. L., and Kluger, R. (2004) Catalysis by Enzyme Conformational Change, Top. Curr. Chem. 238, 113-136.
-
(2004)
Top. Curr. Chem
, vol.238
, pp. 113-136
-
-
Gao, J.1
Byun, K.L.2
Kluger, R.3
-
109
-
-
4344567022
-
Sensitivity of Molecular Dynamics Simulations to the Choice of the X-Ray Structure used to Model an Enzymatic Reaction
-
Garcia-Viloca, M., Poulsen, T. D., Truhlar, D. G., and Gao, J. (2004) Sensitivity of Molecular Dynamics Simulations to the Choice of the X-Ray Structure used to Model an Enzymatic Reaction, Protein Sci. 13, 2341-2354.
-
(2004)
Protein Sci
, vol.13
, pp. 2341-2354
-
-
Garcia-Viloca, M.1
Poulsen, T.D.2
Truhlar, D.G.3
Gao, J.4
-
110
-
-
84967360407
-
-
3rd ed, World Scientific, Singapore, River Edge, NJ
-
Kleinert, H. (2004) Path integrals in quantum mechanics, statistics, polymer physics, and financial markets, 3rd ed., World Scientific, Singapore, River Edge, NJ.
-
(2004)
Path integrals in quantum mechanics, statistics, polymer physics, and financial markets
-
-
Kleinert, H.1
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