-
2
-
-
60349127442
-
Qm/mm methods for biomolecular systems
-
Senn HM, Thiel W (2009) QM/MM methods for biomolecular systems. Angew Chem Int Ed Engl 48:1198-1229
-
(2009)
Angew Chem Int Ed Engl
, vol.48
, pp. 1198-1229
-
-
Senn, H.M.1
Thiel, W.2
-
3
-
-
58949095484
-
Computational enzymology: Insight into biological catalysts from modelling
-
van der Kamp MW, Mulholland AJ (2008) Computational enzymology: insight into biological catalysts from modelling. Nat Prod Rep 25:1001-1014
-
(2008)
Nat Prod Rep
, vol.25
, pp. 1001-1014
-
-
Van Der Kamp, M.W.1
Mulholland, A.J.2
-
4
-
-
27144494583
-
Modelling enzyme reaction mechanisms, specificity and catalysis
-
Mulholland AJ (2005) Modelling enzyme reaction mechanisms, specificity and catalysis. Drug Discov Today 10:1393-1402
-
(2005)
Drug Discov Today
, vol.10
, pp. 1393-1402
-
-
Mulholland, A.J.1
-
5
-
-
0346726109
-
How enzymes work: Analysis by modern rate theory and computer simulations
-
Garcia-Viloca M, Gao J, Karplus M, Truhlar DG (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
-
6
-
-
0041876227
-
Computer simulations of enzyme catalysis: Methods, progress, and insights
-
Warshel A (2003) Computer simulations of enzyme catalysis: methods, progress, and insights. Annu Rev Biophys Biomol Struct 32:425-443
-
(2003)
Annu Rev Biophys Biomol Struct
, vol.32
, pp. 425-443
-
-
Warshel, A.1
-
7
-
-
21244497608
-
Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (qm/mm) methods for studying enzymatic catalysis
-
Friesner RA, 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
-
8
-
-
1642410886
-
Theoretical insights in enzyme catalysis
-
Martí S, Roca M, Andrés J, Moliner V, Silla E, Tunón I, Bertrán J (2004) Theoretical insights in enzyme catalysis. Chem Soc Rev 33:98-107
-
(2004)
Chem Soc Rev
, vol.33
, pp. 98-107
-
-
Martí, S.1
Roca, M.2
Andrés, J.3
Moliner, V.4
Silla, E.5
Tunón, I.6
Bertrán, J.7
-
9
-
-
33748263628
-
Quantum chemical modeling of enzyme active sites and reaction mechanisms
-
Himo F (2006) Quantum chemical modeling of enzyme active sites and reaction mechanisms. Theor Chem Acc 116:232-240
-
(2006)
Theor Chem Acc
, vol.116
, pp. 232-240
-
-
Himo, F.1
-
10
-
-
33748633480
-
Electrostatic basis for enzyme catalysis
-
Warshel A, Sharma PK, Kato M, Xiang Y, Liu HB, Olsson MHM (2006) Electrostatic basis for enzyme catalysis. Chem Rev 106:3210-3235
-
(2006)
Chem Rev
, vol.106
, pp. 3210-3235
-
-
Warshel, A.1
Sharma, P.K.2
Kato, M.3
Xiang, Y.4
Liu, H.B.5
Olsson, M.H.M.6
-
12
-
-
0027506191
-
Computer modelling of enzyme catalysed reaction mechanisms
-
Mulholland AJ, Grant GH, Richards WG (1993) Computer modelling of enzyme catalysed reaction mechanisms. Protein Eng 6:133-147
-
(1993)
Protein Eng
, vol.6
, pp. 133-147
-
-
Mulholland, A.J.1
Grant, G.H.2
Richards, W.G.3
-
14
-
-
4243810035
-
Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches
-
A ° qvist J, 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
-
15
-
-
0017100947
-
Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme
-
Warshel A, Levitt M (1976) Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J Mol Biol 103:227-249
-
(1976)
J Mol Biol
, vol.103
, pp. 227-249
-
-
Warshel, A.1
Levitt, M.2
-
17
-
-
33750478314
-
High accuracy computation of reaction barriers in enzymes
-
Claeyssens F, Harvey JN, Manby FR, Mata RA, Mulholland AJ, Ranaghan KE, Schultz M, Thiel S, Thiel W, Werner H-J (2006) High accuracy computation of reaction barriers in enzymes. Angew Chem Int Ed 45:6856-6859
-
(2006)
Angew Chem Int Ed
, vol.45
, pp. 6856-6859
-
-
Claeyssens, F.1
Harvey, J.N.2
Manby, F.R.3
Mata, R.A.4
Mulholland, A.J.5
Ranaghan, K.E.6
Schultz, M.7
Thiel, S.8
Thiel, W.9
Werner, H.-J.10
-
18
-
-
34547659973
-
Chemical accuracy in qm/mm calculations on enzyme-catalysed reactions
-
Mulholland AJ (2007) Chemical accuracy in QM/MM calculations on enzyme-catalysed reactions. Chem Cent J 1:19
-
(2007)
Chem Cent J
, vol.1
, pp. 19
-
-
Mulholland, A.J.1
-
19
-
-
33845946492
-
Computer modeling of enzyme catalysis and its relationship to concepts in physical organic chemistry
-
Braun-Sand S, Olsson MHM, Warshel A (2005) Computer modeling of enzyme catalysis and its relationship to concepts in physical organic chemistry. Adv Phys Org Chem 40:201-245
-
(2005)
Adv Phys Org Chem
, vol.40
, pp. 201-245
-
-
Braun-Sand, S.1
Olsson, M.H.M.2
Warshel, A.3
-
20
-
-
0035939953
-
Catalysis by hen egg white lysozyme proceeds via a covalent intermediate
-
Vocadlo DJ, Davies GJ, Laine R, Withers SG (2001) Catalysis by hen egg white lysozyme proceeds via a covalent intermediate. Nature 412:3835-3838
-
(2001)
Nature
, vol.412
, pp. 3835-3838
-
-
Vocadlo, D.J.1
Davies, G.J.2
Laine, R.3
Withers, S.G.4
-
21
-
-
52449116184
-
Qm/mm simulations predict a covalent intermediate in the hen egg white lysozyme reaction with its natural substrate
-
Bowman AL, Grant IM, Mulholland AJ (2008) QM/MM simulations predict a covalent intermediate in the hen egg white lysozyme reaction with its natural substrate. Chem Commun 7:4425-4427
-
(2008)
Chem Commun
, vol.7
, pp. 4425-4427
-
-
Bowman, A.L.1
Grant, I.M.2
Mulholland, A.J.3
-
22
-
-
0032475836
-
The low barrier hydrogen bond in enzymatic catalysis
-
Cleland WW, Frey PA, Gerlt JA (1998) The low barrier hydrogen bond in enzymatic catalysis. J Biol Chem 273:25529-25532
-
(1998)
J Biol Chem
, vol.273
, pp. 25529-25532
-
-
Cleland, W.W.1
Frey, P.A.2
Gerlt, J.A.3
-
23
-
-
0034716340
-
Ab initio qm/mm study of the citrate synthase mechanism: A low-barrier hydrogen bond is not involved
-
Mulholland AJ, Lyne PD, Karplus M (2000) Ab initio QM/MM study of the citrate synthase mechanism: a low-barrier hydrogen bond is not involved. J Am Chem Soc 122:534-535
-
(2000)
J Am Chem Soc
, vol.122
, pp. 534-535
-
-
Mulholland, A.J.1
Lyne, P.D.2
Karplus, M.3
-
24
-
-
2442606719
-
The low barrier hydrogen bond (lbhb) proposal revisited: The case of the asp his pair in serine proteases
-
Schutz CN,Warshel A (2004) The low barrier hydrogen bond (LBHB) proposal revisited: the case of the Asp His pair in serine proteases. Proteins 55:711-723
-
(2004)
Proteins
, vol.55
, pp. 711-723
-
-
Schutz, C.N.1
Warshel, A.2
-
25
-
-
0038112245
-
A predictive model of strong hydrogen bonding in proteins: The nd1-h-od1 hydrogen bond in low-ph a-chymotrypsin and a-lytic protease
-
Molina PA, Jensen JH (2003) A predictive model of strong hydrogen bonding in proteins: the Nd1-H-Od1 hydrogen bond in low-pH a-chymotrypsin and a-lytic protease. J Phys Chem B 107:6226-6233
-
(2003)
J Phys Chem B
, vol.107
, pp. 6226-6233
-
-
Molina, P.A.1
Jensen, J.H.2
-
26
-
-
0042355696
-
Just a near attack conformer for catalysis (chorismate to prephenate rearrangements in water, antibody, enzymes, and their mutants)
-
Hur S, Bruice TC (2003) Just a near attack conformer for catalysis (chorismate to prephenate rearrangements in water, antibody, enzymes, and their mutants). J Am Chem Soc 125:10540-10542
-
(2003)
J Am Chem Soc
, vol.125
, pp. 10540-10542
-
-
Hur, S.1
Bruice, T.C.2
-
27
-
-
2942739060
-
Conformational effects in enzyme catalysis: Qm/mm free energy calculation of the 'nac' contribution in chorismate mutase
-
Ranaghan KE, Mulholland AJ (2004) Conformational effects in enzyme catalysis: QM/MM free energy calculation of the 'NAC' contribution in chorismate mutase. Chem Commun 10:1238-1239
-
(2004)
Chem Commun
, vol.10
, pp. 1238-1239
-
-
Ranaghan, K.E.1
Mulholland, A.J.2
-
28
-
-
33646935697
-
Dynamical contributions to enzyme catalysis: Critical tests of a popular hypothesis
-
Olsson MH, Parson WW, Warshel A (2006) Dynamical contributions to enzyme catalysis: critical tests of a popular hypothesis. Chem Rev 106:1737-1756
-
(2006)
Chem Rev
, vol.106
, pp. 1737-1756
-
-
Olsson, M.H.1
Parson, W.W.2
Warshel, A.3
-
29
-
-
33748349036
-
Hydride transfer catalyzed by escherichia coli and bacillus subtilis dihydrofolate reductase: Coupled motions and distal mutations
-
Hammes-Schiffer S, Watney JB (2006) Hydride transfer catalyzed by Escherichia coli and Bacillus subtilis dihydrofolate reductase: Coupled motions and distal mutations. Phil Trans Roy Soc B 361:1365-1373
-
(2006)
Phil Trans Roy Soc B
, vol.361
, pp. 1365-1373
-
-
Hammes-Schiffer, S.1
Watney, J.B.2
-
30
-
-
33645801770
-
Atomic description of an enzyme reaction dominated by proton tunneling
-
Masgrau L, Roujeinikova A, Johannissen LO, Hothi P, Basran J, Ranaghan KE, Mulholland AJ, Sutcliffe MJ, Scrutton NS, Leys D (2006) Atomic description of an enzyme reaction dominated by proton tunneling. Science 312:237-241
-
(2006)
Science
, vol.312
, pp. 237-241
-
-
Masgrau, L.1
Roujeinikova, A.2
Johannissen, L.O.3
Hothi, P.4
Basran, J.5
Ranaghan, K.E.6
Mulholland, A.J.7
Sutcliffe, M.J.8
Scrutton, N.S.9
Leys, D.10
-
31
-
-
33846047459
-
Proton-coupled electron transfer in soybean lipoxygenase: Dynamical behavior and temperature dependence of kinetic isotope effects
-
Hatcher E, Soudackov AV, Hammes-Schiffer S (2007) Proton-coupled electron transfer in soybean lipoxygenase: dynamical behavior and temperature dependence of kinetic isotope effects. J Am Chem Soc 129:187-196
-
(2007)
J Am Chem Soc
, vol.129
, pp. 187-196
-
-
Hatcher, E.1
Soudackov, A.V.2
Hammes-Schiffer, S.3
-
32
-
-
33748367252
-
Arrhenius curves of hydrogen transfers: Tunnel effects, isotope effects and effects of preequilibria
-
Limbach HH, Lopez JM, Kohen A (2006) Arrhenius curves of hydrogen transfers: tunnel effects, isotope effects and effects of preequilibria. Phil Trans Roy Soc B 361:1399-1415
-
(2006)
Phil Trans Roy Soc B
, vol.361
, pp. 1399-1415
-
-
Limbach, H.H.1
Lopez, J.M.2
Kohen, A.3
-
33
-
-
33748601471
-
Tunneling and dynamics in enzymatic hydride transfer
-
Nagel ZD, Klinman JP (2006) Tunneling and dynamics in enzymatic hydride transfer. Chem Rev 106:3095-3118
-
(2006)
Chem Rev
, vol.106
, pp. 3095-3118
-
-
Nagel, Z.D.1
Klinman, J.P.2
-
34
-
-
0034710867
-
How important are entropic contributions to enzyme catalysis?
-
Villa J, Strajbl M, Glennon TM, Sham YY, Chu ZT, Warshel A (2000) How important are entropic contributions to enzyme catalysis? Proc Natl Acad Sci USA 97:11899-11904
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 11899-11904
-
-
Villa, J.1
Strajbl, M.2
Glennon, T.M.3
Sham, Y.Y.4
Chu, Z.T.5
Warshel, A.6
-
36
-
-
0037422356
-
Ab initio qm/mm modeling of the hydroxylation step in p-hydroxybenzoate hydroxylase
-
Ridder L, Harvey JN, Rietjens IMCM, Vervoort J, Mulholland AJ (2003) Ab initio QM/MM modeling of the hydroxylation step in p-hydroxybenzoate hydroxylase. J Phys Chem B 107:2118-2126
-
(2003)
J Phys Chem B
, vol.107
, pp. 2118-2126
-
-
Ridder, L.1
Harvey, J.N.2
Imcm, R.3
Vervoort, J.4
Mulholland, A.J.5
-
37
-
-
0034644411
-
A quantum mechanical/molecular mechanical study of the hydroxylation of phenol and halogenated derivatives by phenol hydroxylase
-
Ridder L, Mulholland AJ, Rietjens IMCM, Vervoort J (2000) A quantum mechanical/molecular mechanical study of the hydroxylation of phenol and halogenated derivatives by phenol hydroxylase. J Am Chem Soc 122:8728-8738
-
(2000)
J Am Chem Soc
, vol.122
, pp. 8728-8738
-
-
Ridder, L.1
Mulholland, A.J.2
Imcm, R.3
Vervoort, J.4
-
38
-
-
8744303696
-
Prediction of structure, substrate binding mode, mechanism, and rate for a malaria protease with a novel type of active site
-
Bjelic S, A ° qvist J (2004) Prediction of structure, substrate binding mode, mechanism, and rate for a malaria protease with a novel type of active site. Biochemistry 43:14521-14528
-
(2004)
Biochemistry
, vol.43
, pp. 14521-14528
-
-
Bjelic S, A.1
Qvist, J.2
-
39
-
-
0038016725
-
Influence of structural fluctuation on enzyme reaction energy barriers in combined quantum mechanical/molecular mechanical studies
-
Zhang YK, Kua J, McCammon JA (2003) Influence of structural fluctuation on enzyme reaction energy barriers in combined quantum mechanical/molecular mechanical studies. J Phys Chem B 107:4459-4463
-
(2003)
J Phys Chem B
, vol.107
, pp. 4459-4463
-
-
Zhang, Y.K.1
Kua, J.2
McCammon, J.A.3
-
40
-
-
0036025446
-
Quantum mechanical methods for enzyme kinetics
-
Gao JL, Truhlar DG (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.L.1
Truhlar, D.G.2
-
41
-
-
12944292929
-
Protein structural transitions and their functional role
-
Karplus M, Gao YQ, Ma JP, van der Vaart A, Yang W (2005) Protein structural transitions and their functional role. Phil Trans R Soc A 363:331-355
-
(2005)
Phil Trans R Soc A
, vol.363
, pp. 331-355
-
-
Karplus, M.1
Gao, Y.Q.2
Ma, J.P.3
Van Der Vaart, A.4
Yang, W.5
-
43
-
-
9344245168
-
Solute solvent dynamics and energetics in enzyme catalysis: The s(n)2 reaction of dehalogenase as a general benchmark
-
Olsson MHM, Warshel A (2004) Solute solvent dynamics and energetics in enzyme catalysis: the S(N)2 reaction of dehalogenase as a general benchmark. J Am Chem Soc 126:15167-15179
-
(2004)
J Am Chem Soc
, vol.126
, pp. 15167-15179
-
-
Olsson, M.H.M.1
Warshel, A.2
-
44
-
-
4744343045
-
Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair
-
Wolf-Watz M, Thai V, Henzler-Wildman K, Hadjipaylou G, Eisenmesser EZ, Kern D (2004) Linkage between dynamics and catalysis in a thermophilic- mesophilic enzyme pair. Nat Struct Mol Biol 11:945-949
-
(2004)
Nat Struct Mol Biol
, vol.11
, pp. 945-949
-
-
Wolf-Watz, M.1
Thai, V.2
Henzler-Wildman, K.3
Hadjipaylou, G.4
Eisenmesser, E.Z.5
Kern, D.6
-
45
-
-
0033519723
-
Enzyme dynamics and hydrogen tunneling in a thermophilic alcohol dehydrogenase
-
Kohen A, Cannio R, Bartolucci S, Klinman JP (1999) Enzyme dynamics and hydrogen tunneling in a thermophilic alcohol dehydrogenase. Nature 399:496-499
-
(1999)
Nature
, vol.399
, pp. 496-499
-
-
Kohen, A.1
Cannio, R.2
Bartolucci, S.3
Klinman, J.P.4
-
46
-
-
33748357971
-
Hydrogen tunnelling in enzyme-catalysed h-transfer reactions: Flavoprotein and quinoprotein systems
-
Sutcliffe MJ,Masgrau L, Roujeinikova A, Johannissen LO, Hothi P, Basran J, Ranaghan KE, Mulholland AJ, Leys D, Scrutton NS (2006) Hydrogen tunnelling in enzyme-catalysed H-transfer reactions: flavoprotein and quinoprotein systems. Phil Trans Roy Soc B 361:1375-1386
-
(2006)
Phil Trans Roy Soc B
, vol.361
, pp. 1375-1386
-
-
Sutcliffe, M.J.1
Masgrau, L.2
Roujeinikova, A.3
Johannissen, L.O.4
Hothi, P.5
Basran, J.6
Ranaghan, K.E.7
Mulholland, A.J.8
Leys, D.9
Scrutton, N.S.10
-
47
-
-
77949829432
-
Computer simulations of quantum tunnelling in enzyme-catalysed hydrogen transfer reactions
-
Ranaghan KE, Mulholland AJ (2010) Computer simulations of quantum tunnelling in enzyme-catalysed hydrogen transfer reactions. Interdiscip Sci 2:78-97
-
(2010)
Interdiscip Sci
, vol.2
, pp. 78-97
-
-
Ranaghan, K.E.1
Mulholland, A.J.2
-
48
-
-
37849017099
-
Cooperative symmetric to asymmetric conformational transition of the apoform of scavenger decapping enzyme revealed by simulations
-
Pentikainen U, Pentikainen OT, Mulholland AJ (2008) Cooperative symmetric to asymmetric conformational transition of the apoform of scavenger decapping enzyme revealed by simulations. Proteins 70:498-508
-
(2008)
Proteins
, vol.70
, pp. 498-508
-
-
Pentikainen, U.1
Pentikainen, O.T.2
Mulholland, A.J.3
-
49
-
-
33846413566
-
Conformational effects in enzyme catalysis: Reaction via a high energy conformation in fatty acid amide hydrolase
-
Lodola A, Mor M, Zurek J, Tarzia G, Piomelli D, Harvey JN, Mulholland AJ (2007) Conformational effects in enzyme catalysis: reaction via a high energy conformation in fatty acid amide hydrolase. Biophys J 92: L20-L22
-
(2007)
Biophys J
, vol.92
-
-
Lodola, A.1
Mor, M.2
Zurek, J.3
Tarzia, G.4
Piomelli, D.5
Harvey, J.N.6
Mulholland, A.J.7
-
50
-
-
23444454552
-
The amber biomolecular simulation programs
-
Case DA, Cheatham TE III, Darden T, Gohlke H, Luo R, Merz KM Jr., Onufriev A, Simmerling C, Wang B, Woods R (2005) The AMBER biomolecular simulation programs. J Comput Chem 26:1668-1688 (see http://amber.scripps.edu/)
-
(2005)
J Comput Chem
, vol.26
, pp. 1668-1688
-
-
Case, D.A.1
Cheatham III, T.E.2
Darden, T.3
Gohlke, H.4
Luo, R.5
Merz Jr., K.M.6
Onufriev, A.7
Simmerling, C.8
Wang, B.9
Woods, R.10
-
51
-
-
84986512474
-
Charmm: A program for macromolecular energy, minimization, and dynamics calculations
-
(See also
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4:187-217, (See also http://www.charmm.org)
-
(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
-
52
-
-
0008819754
-
The gromos biomolecular simulation program package
-
(see
-
Scott WRP, Hunenberger PH, Tironi IG, Mark AE, Billeter SR, Fennen J, Torda AE, Huber T, Kruger P, van Gunsteren WF (1999) The GROMOS biomolecular simulation program package. J Phys Chem A 103:3596-3607, (see http://www.igc.ethz. ch/gromos/gromos.html)
-
(1999)
J Phys Chem A
, vol.103
, pp. 3596-3607
-
-
Scott, W.R.P.1
Hunenberger, P.H.2
Tironi, I.G.3
Mark, A.E.4
Billeter, S.R.5
Fennen, J.6
Torda, A.E.7
Huber, T.8
Kruger, P.9
Van Gunsteren, W.F.10
-
53
-
-
27344436659
-
Scalable molecular dynamics with namd
-
(see
-
Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale L, Schulten K (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26:1781-1802, (see http://www.ks.uiuc. edu/Research/namd/)
-
(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, R.D.8
Kale, L.9
Schulten, K.10
-
54
-
-
84988112508
-
An efficient newton-likemethod for molecular mechanics energy minimization of large molecules
-
(see
-
Ponder JW, Richards FM (1987) An efficient newton-likemethod for molecular mechanics energy minimization of large molecules. J Comput Chem 8:1016-1024, (see http://dasher.wustl.edu/tinker/)
-
(1987)
J Comput Chem
, vol.8
, pp. 1016-1024
-
-
Ponder, J.W.1
Richards, F.M.2
-
55
-
-
0029912748
-
Development and testing of the opls all-Atom force field on conformational energetics and properties of organic liquids
-
Jorgensen WL, Maxwell DS, Tirado-Rives J (1996) Development and testing of the OPLS all-Atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 118:11225-11236
-
(1996)
J Am Chem Soc
, vol.118
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
56
-
-
0035913529
-
Evaluation and reparametrization of the oplsaa force field for proteins via comparison with accurate quantum chemical calculations on peptides
-
Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL (2001) Evaluation and reparametrization of the OPLSAA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem B 105:6474-6487
-
(2001)
J Phys Chem B
, vol.105
, pp. 6474-6487
-
-
Kaminski, G.A.1
Friesner, R.A.2
Tirado-Rives, J.3
Jorgensen, W.L.4
-
57
-
-
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 (1998) All-Atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 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
Reiher III, W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiórkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
58
-
-
0029011701
-
A 2nd generation force-field for the simulation of proteins, nucleic-Acids, and organic molecules
-
Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1995) A 2nd generation force-field for the simulation of proteins, nucleic-Acids, and organic molecules. J Am Chem Soc 117:5179-5197
-
(1995)
J Am Chem Soc
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
59
-
-
77956731325
-
Empirical force fields for proteins: Current status and future directions
-
Mackerell AD (2005) Empirical force fields for proteins: current status and future directions. Ann Rep Comp Chem 1:91-111
-
(2005)
Ann Rep Comp Chem
, vol.1
, pp. 91-111
-
-
Mackerell, A.D.1
-
60
-
-
0242443693
-
Force fields for protein simulations
-
Ponder JW, Case DA (2003) Force fields for protein simulations. Adv Protein Chem 66:27-75
-
(2003)
Adv Protein Chem
, vol.66
, pp. 27-75
-
-
Ponder, J.W.1
Case, D.A.2
-
61
-
-
33847651004
-
Molecular modeling and atomistic simulation of nucleic acids
-
Cheatham TE III (2005) Molecular modeling and atomistic simulation of nucleic acids. Ann Rep Comp Chem 1:75-90
-
(2005)
Ann Rep Comp Chem
, vol.1
, pp. 75-90
-
-
Cheatham III, T.E.1
-
62
-
-
2942547665
-
Simulation and modeling of nucleic acid structure, dynamics and interactions
-
Cheatham TE III (2004) Simulation and modeling of nucleic acid structure, dynamics and interactions. Curr Opin Struct Biol 14:360-367
-
(2004)
Curr Opin Struct Biol
, vol.14
, pp. 360-367
-
-
Cheatham III, T.E.1
-
63
-
-
0348244547
-
All-Atom empirical force field for nucleic acids: I parameter optimization based on small molecule and condensed phase macromolecular target data
-
Foloppe N, MacKerell AD (2000) All-Atom empirical force field for nucleic acids: I parameter optimization based on small molecule and condensed phase macromolecular target data. J Comput Chem 21:86-104
-
(2000)
J Comput Chem
, vol.21
, pp. 86-104
-
-
Foloppe, N.1
MacKerell, A.D.2
-
64
-
-
0000214231
-
All-Atom empirical force field for nucleic acids: Ii application to molecular dynamics simulations of dna and rna in solution
-
MacKerell AD, Banavali NK (2000) All-Atom empirical force field for nucleic acids: II application to molecular dynamics simulations of DNA and RNA in solution. J Comput Chem 21:105-120
-
(2000)
J Comput Chem
, vol.21
, pp. 105-120
-
-
MacKerell, A.D.1
Banavali, N.K.2
-
65
-
-
0032922174
-
A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat.
-
Cheatham TE, Cieplak P, Kollman PA (1999) A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. J Biomol Struct Dyn 16:845-862
-
(1999)
J Biomol Struct Dyn
, vol.16
, pp. 845-862
-
-
Cheatham, T.E.1
Cieplak, P.2
Kollman, P.A.3
-
66
-
-
0030844208
-
Molecular dynamics simulation of unsaturated lipid bilayers at low hydration: Parameterization and comparison with diffraction studies
-
Feller SE, Yin DX, Pastor RW, MacKerell AD (1997) Molecular dynamics simulation of unsaturated lipid bilayers at low hydration: parameterization and comparison with diffraction studies. Biophys J 73:2269-2279
-
(1997)
Biophys J
, vol.73
, pp. 2269-2279
-
-
Feller, S.E.1
Yin, D.X.2
Pastor, R.W.3
MacKerell, A.D.4
-
67
-
-
18744387415
-
Potential energy functions for atomic-level simulations of water and organic and biomolecular systems
-
JorgensenWL,Tirado-Rives J (2005) Potential energy functions for atomic-level simulations of water and organic and biomolecular systems. Proc Natl Acad Sci USA 102:6665-6670
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 6665-6670
-
-
Jorgensen, W.L.1
Tirado-Rives, J.2
-
68
-
-
24944460249
-
Structure and dynamics of the solvation of bovine pancreatic trypsin inhibitor in explicit water: A comparative study of the effects of solvent and protein polarizability
-
Kim BC, Young T, Harder E, Friesner RA, Berne BJ (2005) Structure and dynamics of the solvation of bovine pancreatic trypsin inhibitor in explicit water: a comparative study of the effects of solvent and protein polarizability. J Phys Chem B 109:16529-16538
-
(2005)
J Phys Chem B
, vol.109
, pp. 16529-16538
-
-
Kim, B.C.1
Young, T.2
Harder, E.3
Friesner, R.A.4
Berne, B.J.5
-
69
-
-
77149168226
-
Compatibility of quantum chemical methods and empirical (mm) water models in quantum mechanics/molecular mechanics liquid water simulations
-
Shaw KE, Woods CJ, Mulholland AJ (2010) Compatibility of quantum chemical methods and empirical (MM) water models in quantum mechanics/molecular mechanics liquid water simulations. J Phys Chem Lett 1:219-223
-
(2010)
J Phys Chem Lett
, vol.1
, pp. 219-223
-
-
Shaw, K.E.1
Woods, C.J.2
Mulholland, A.J.3
-
70
-
-
0004104842
-
Solvent as catalyst: Computational studies of organic reactions in solution
-
In: Truhlar DG, Morokuma K (eds) American Chemical Society, Washington DC
-
Lim D, Jenson J, Repasky MP, Jorgensen WL (1999) Solvent as catalyst: computational studies of organic reactions in solution. In: Truhlar DG, Morokuma K (eds) Transition state modeling for catalysis. American Chemical Society, Washington DC
-
(1999)
Transition State Modeling For Catalysis.
-
-
Lim, D.1
Jenson, J.2
Repasky, M.P.3
Jorgensen, W.L.4
-
71
-
-
11644294259
-
Hybrid ab initio quantum mechanics molecular mechanics calculations of free energy surfaces for enzymatic reactions: The nucleophilic attack in subtilisin
-
Bentzien J, Muller RP, Florian J, Warshel A (1998) Hybrid ab initio quantum mechanics molecular mechanics calculations of free energy surfaces for enzymatic reactions: the nucleophilic attack in subtilisin. J Phys Chem B 102:2293-2301
-
(1998)
J Phys Chem B
, vol.102
, pp. 2293-2301
-
-
Bentzien, J.1
Muller, R.P.2
Florian, J.3
Warshel, A.4
-
73
-
-
0035940264
-
Energetics and dynamics of enzymatic reactions
-
Villa J, 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
-
74
-
-
33847006589
-
Electrostatic contributions to binding of transition state analogues can be different from the corresponding contributions to catalysis: Phenolates binding to the oxyanion hole of ketosteroid isomerase
-
Warshel A, Sharma PK, Chu ZT, A ° qvist J (2007) Electrostatic contributions to binding of transition state analogues can be different from the corresponding contributions to catalysis: phenolates binding to the oxyanion hole of ketosteroid isomerase. Biochemistry 46:1466-1476
-
(2007)
Biochemistry
, vol.46
, pp. 1466-1476
-
-
Warshel, A.1
Sharma, P.K.2
Chu, Z.T.3
Aqvist, J.4
-
75
-
-
33746869326
-
Catalysis and linear free energy relationships in aspartic proteases
-
Bjelic S, A ° qvist J (2006) Catalysis and linear free energy relationships in aspartic proteases. Biochemistry 45:7709-7723
-
(2006)
Biochemistry
, vol.45
, pp. 7709-7723
-
-
Bjelic, S.1
Aqvist, J.2
-
76
-
-
24644461086
-
Mechanism of peptide bond synthesis on the ribosome
-
Trobro S,A ° qvist J (2005) Mechanism of peptide bond synthesis on the ribosome. Proc Natl Acad Sci USA 102:12395-12400
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 12395-12400
-
-
Trobro, S.1
Aqvist, J.2
-
77
-
-
23944472625
-
What are the roles of substrate-Assisted catalysis and proximity effects in peptide bond formation by the ribosome?
-
Sharma PK, Xiang Y, Katom M, Warshel A (2005) What are the roles of substrate-Assisted catalysis and proximity effects in peptide bond formation by the ribosome? Biochemistry 44:11307-11314
-
(2005)
Biochemistry
, vol.44
, pp. 11307-11314
-
-
Sharma, P.K.1
Xiang, Y.2
Katom, M.3
Warshel, A.4
-
78
-
-
1842839777
-
Quantumclassical simulation methods for hydrogen transfer in enzymes: A case study of dihydrofolate reductase
-
Hammes-Schiffer S (2004) Quantumclassical simulation methods for hydrogen transfer in enzymes: a case study of dihydrofolate reductase. Curr Opin Struct Biol 14:192-201
-
(2004)
Curr Opin Struct Biol
, vol.14
, pp. 192-201
-
-
Hammes-Schiffer, S.1
-
79
-
-
34547456661
-
Origin of the temperature dependence of isotope effects in enzymatic reactions: The case of dihydrofolate reductase
-
Liu HB, Warshel A (2007) Origin of the temperature dependence of isotope effects in enzymatic reactions: the case of dihydrofolate reductase. J Phys Chem B 111:7852-7861
-
(2007)
J Phys Chem B
, vol.111
, pp. 7852-7861
-
-
Liu, H.B.1
Warshel, A.2
-
80
-
-
34547457947
-
A new paradigm for electrostatic catalysis of radical reactions in vitamin b12 enzymes
-
Sharma PK, Chu ZT, Olsson MHM, Warshel A (2007) A new paradigm for electrostatic catalysis of radical reactions in vitamin B12 enzymes. Proc Natl Acad Sci USA 2007 (104):9661-9666
-
(2007)
Proc Natl Acad Sci USA
, vol.2007
, Issue.104
, pp. 9661-9666
-
-
Sharma, P.K.1
Chu, Z.T.2
Olsson, M.H.M.3
Warshel, A.4
-
81
-
-
0001499720
-
Linear scaling molecular orbital calculations of biological systems using the semiempirical divide and conquer method
-
Van derVaart A, Gogonea V, Dixon SL, Merz KM (2000) Linear scaling molecular orbital calculations of biological systems using the semiempirical divide and conquer method. J Comput Chem 21:1494-1504
-
(2000)
J Comput Chem
, vol.21
, pp. 1494-1504
-
-
Van DerVaart, A.1
Gogonea, V.2
Dixon, S.L.3
Merz, K.M.4
-
82
-
-
4043072686
-
Quantum descriptors for biological macromolecules from linear-scaling electronic structure methods
-
Khandogin J, York DM (2004) Quantum descriptors for biological macromolecules from linear-scaling electronic structure methods. Proteins 56:724-737
-
(2004)
Proteins
, vol.56
, pp. 724-737
-
-
Khandogin, J.1
York, D.M.2
-
83
-
-
0038013705
-
Insights into the regioselectivity and rna-binding affinity of hiv-1 nucleocapsid protein from linear-scaling quantum methods
-
Khandogin J, Musier-Forsyth K, York DM (2003) Insights into the regioselectivity and RNA-binding affinity of HIV-1 nucleocapsid protein from linear-scaling quantum methods. J Mol Biol 330:993-1004
-
(2003)
J Mol Biol
, vol.330
, pp. 993-1004
-
-
Khandogin, J.1
Musier-Forsyth, K.2
York, D.M.3
-
84
-
-
78149341694
-
Inclusion of dispersion effects significantly improves accuracy of calculated reaction barriers for cytochrome p450 catalyzed reactions
-
Lonsdale R, Harvey JN, Mulholland AJ (2010) Inclusion of dispersion effects significantly improves accuracy of calculated reaction barriers for cytochrome p450 catalyzed reactions. J Phys Chem Lett 1:3232-3237
-
(2010)
J Phys Chem Lett
, vol.1
, pp. 3232-3237
-
-
Lonsdale, R.1
Harvey, J.N.2
Mulholland, A.J.3
-
85
-
-
0038305457
-
Quantum chemical studies of radical-containing enzymes
-
Himo F, Siegbahn PE (2003) Quantum chemical studies of radical-containing enzymes. Chem Rev 103:2421-2456
-
(2003)
Chem Rev
, vol.103
, pp. 2421-2456
-
-
Himo, F.1
Siegbahn, P.E.2
-
86
-
-
67649476220
-
Recent developments of the quantum chemical cluster approach for modeling enzyme reactions
-
Siegbahn PE, Himo F (2009) Recent developments of the quantum chemical cluster approach for modeling enzyme reactions. J Biol Inorg Chem 14:643-651
-
(2009)
J Biol Inorg Chem
, vol.14
, pp. 643-651
-
-
Siegbahn, P.E.1
Himo, F.2
-
87
-
-
0038056330
-
Exploring the quantum mechanical/molecular mechanical replica path method: A pathway optimization of the chorismate to prephenate claisen rearrangement catalyzed by chorismate mutase
-
Woodcock HL, Hodoscek M, Sherwood P, Lee YS, Schaefer HF, Brooks BR (2003) Exploring the quantum mechanical/molecular mechanical replica path method: a pathway optimization of the chorismate to prephenate Claisen rearrangement catalyzed by chorismate mutase. Theor Chem Acc 109:140-148
-
(2003)
Theor Chem Acc
, vol.109
, pp. 140-148
-
-
Woodcock, H.L.1
Hodoscek, M.2
Sherwood, P.3
Lee, Y.S.4
Schaefer, H.F.5
Brooks, B.R.6
-
88
-
-
84986513644
-
A combined quantum-mechanical and molecular mechanical potential for molecular-dynamics simulations
-
Field MJ, Bash PA, 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
-
89
-
-
0000218385
-
A hybrid qm-mm potential employing hartree-fock or density functional methods in the quantum region
-
Lyne PD, Hodoscek M, Karplus M (1999) A hybrid QM-MM potential employing Hartree-Fock or density functional methods in the quantum region. J Phys Chem A 103:3462-3471
-
(1999)
J Phys Chem A
, vol.103
, pp. 3462-3471
-
-
Lyne, P.D.1
Hodoscek, M.2
Karplus, M.3
-
90
-
-
0035138648
-
A qm/mm implementation of the self-consistent charge density functional tight binding (scc-dftb) method
-
Cui Q, Elstner M, Kaxiras E, Frauenheim T, Karplus M (2001) A QM/MM implementation of the self-consistent charge density functional tight binding (SCC-DFTB) method. J Phys Chem B 105:569-585
-
(2001)
J Phys Chem B
, vol.105
, pp. 569-585
-
-
Cui, Q.1
Elstner, M.2
Kaxiras, E.3
Frauenheim, T.4
Karplus, M.5
-
91
-
-
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 (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
-
92
-
-
2442562626
-
Geometry optimization and transition state search in enzymes: Different options in the microiterative method
-
Prat-Resina X, Bofill JM, Gonzalez-Lafont A, Lluch JM (2004) Geometry optimization and transition state search in enzymes: different options in the microiterative method. Int J Quantum Chem 98:367-377
-
(2004)
Int J Quantum Chem
, vol.98
, pp. 367-377
-
-
Prat-Resina, X.1
Bofill, J.M.2
Gonzalez-Lafont, A.3
Lluch, J.M.4
-
93
-
-
0037151638
-
Quantum mechanical/molecular mechanical free energy simulations of the glutathione s-transferase (m1-1) reaction with phenanthrene 9,10-oxide
-
Ridder L, Rietjens IMCM, Vervoort J, Mulholland AJ (2002) Quantum mechanical/molecular mechanical free energy simulations of the glutathione S-transferase (M1-1) reaction with phenanthrene 9,10-oxide. J Am Chem Soc 124:9926-9936
-
(2002)
J Am Chem Soc
, vol.124
, pp. 9926-9936
-
-
Ridder, L.1
Imcm, R.2
Vervoort, J.3
Mulholland, A.J.4
-
94
-
-
2342565009
-
Transition state stabilization and substrate strain in enzyme catalysis: Ab initio qm/mm modelling of the chorismate mutase reaction
-
Ranaghan KE, Ridder L, Szefczyk B, Sokalski WA, Hermann JC, Mulholland AJ (2004) Transition state stabilization and substrate strain in enzyme catalysis: ab initio QM/MM modelling of the chorismate mutase reaction. Org Biomol Chem 2:968-980
-
(2004)
Org Biomol Chem
, vol.2
, pp. 968-980
-
-
Ranaghan, K.E.1
Ridder, L.2
Szefczyk, B.3
Sokalski, W.A.4
Hermann, J.C.5
Mulholland, A.J.6
-
95
-
-
25444523794
-
Qm/mm modelling of oleamide hydrolysis in fatty acid amide hydrolase (faah) reveals a new mechanism of nucleophile activation
-
Lodola A, Mor M, Hermann JC, Tarzia G, Piomelli D, Mulholland AJ (2005) QM/MM modelling of oleamide hydrolysis in fatty acid amide hydrolase (FAAH) reveals a new mechanism of nucleophile activation. Chem Commun 35:4399-4401
-
(2005)
Chem Commun
, vol.35
, pp. 4399-4401
-
-
Lodola, A.1
Mor, M.2
Hermann, J.C.3
Tarzia, G.4
Piomelli, D.5
Mulholland, A.J.6
-
96
-
-
25844473576
-
Pka calculations in solution and proteins with qm/mm free energy perturbation simulations: A quantitative test of qm/mm protocols
-
Riccardi D, Schaefer P, Cui Q (2005) pKa calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols. J Phys Chem B 109:17715-17733
-
(2005)
J Phys Chem B
, vol.109
, pp. 17715-17733
-
-
Riccardi, D.1
Schaefer, P.2
Cui, Q.3
-
97
-
-
0942276314
-
A quantum mechanics-based scoring function: Study of zinc ion-mediated ligand binding
-
Raha K, Merz KM (2004) A quantum mechanics-based scoring function: study of zinc ion-mediated ligand binding. J Am Chem Soc 126:1020-1021
-
(2004)
J Am Chem Soc
, vol.126
, pp. 1020-1021
-
-
Raha, K.1
Merz, K.M.2
-
98
-
-
0345713551
-
Hybrid models for combined quantum mechanical and molecular mechanical approaches
-
Bakowies D, 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
-
99
-
-
31144441067
-
Oniom: A multilayered 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 RDJ, Matsubara T, Sieber S, Morokuma K (1996) ONIOM: A multilayered 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
-
100
-
-
0000473603
-
Adjusted connection atoms for combined quantum mechanical and molecular mechanical methods
-
Antes I, Thiel W (1999) Adjusted connection atoms for combined quantum mechanical and molecular mechanical methods. J Phys Chem A 103:9290-9295
-
(1999)
J Phys Chem A
, vol.103
, pp. 9290-9295
-
-
Antes, I.1
Thiel, W.2
-
101
-
-
34547236888
-
The first hyperpolarizability of p-nitroaniline in 1,4-dioxane: A quantum mechanical/molecular mechanics study
-
Art. No 074307
-
Jensen L, van Duijnen PT (2005) The first hyperpolarizability of p-nitroaniline in 1,4-dioxane: a quantum mechanical/molecular mechanics study. J Chem Phys 123:Art. No. 074307
-
(2005)
J Chem Phys
, vol.123
-
-
Jensen, L.1
Van Duijnen, P.T.2
-
102
-
-
0037181354
-
Quantum mechanics/molecular mechanics studies of triosephosphate isomerase-catalyzed reactions: Effect of geometry and tunneling on proton-transfer rate constants
-
Cui Q, Karplus M (2002) Quantum mechanics/molecular mechanics studies of triosephosphate isomerase-catalyzed reactions: effect of geometry and tunneling on proton-transfer rate constants. J Am Chem Soc 124:3093-3124
-
(2002)
J Am Chem Soc
, vol.124
, pp. 3093-3124
-
-
Cui, Q.1
Karplus, M.2
-
103
-
-
2642585833
-
Importance of van der Waals interactions in QM/MM simulations
-
Riccardi D, Li GH, CuiQ (2004) Importance of van der Waals interactions in QM/MM simulations. J Phys Chem B 108:6467-6478
-
(2004)
J Phys Chem B
, vol.108
, pp. 6467-6478
-
-
Riccardi, D.1
Li, G.H.2
Cui, Q.3
-
104
-
-
0141459794
-
Free energy surface, reaction paths, and kinetic isotope effect of shortchain acyl-coa dehydrogenase
-
Poulsen TD, Garcia-Viloca M, Gao JL, Truhlar DG (2003) Free energy surface, reaction paths, and kinetic isotope effect of shortchain acyl-coa dehydrogenase. J Phys Chem B 107:9567-9578
-
(2003)
J Phys Chem B
, vol.107
, pp. 9567-9578
-
-
Poulsen, T.D.1
Garcia-Viloca, M.2
Gao, J.L.3
Truhlar, D.G.4
-
105
-
-
0003525155
-
-
Wiley, New York
-
Brooks CL III, Karplus M, Pettitt BM (1988) Proteins, a theoretical perspective of dynamics, structure and thermodynamics. Wiley, New York
-
(1988)
Proteins, a theoretical perspective of dynamics, structure and thermodynamics.
-
-
Brooks III, C.L.1
Karplus, M.2
Pettitt, B.M.3
-
106
-
-
19944369519
-
An efficient linear-scaling ewald method for long-range electrostatic interactions in combined qm/mm calculations
-
Nam K, Gao JL, YorkDM(2005) An efficient linear-scaling ewald method for long-range electrostatic interactions in combined QM/MM calculations. J Chem Theory Comput 1:2-13
-
(2005)
J Chem Theory Comput
, vol.1
, pp. 2-13
-
-
Nam, K.1
Gao, J.L.2
York, D.M.3
-
107
-
-
34548059996
-
Reliable treatment of electrostatics in combined qm/mm simulation of macromolecules
-
Art. No 014905
-
Schaefer P, Riccardi D, Cui Q (2005) Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules. J Chem Phys 123:Art. No. 014905
-
(2005)
J Chem Phys
, vol.123
-
-
Schaefer, P.1
Riccardi, D.2
Cui, Q.3
-
108
-
-
0035249196
-
Generalized solvent boundary potentials for computer simulations
-
Im W, Berneche S, Roux B (2001) Generalized solvent boundary potentials for computer simulations. J Chem Phys 114:2924-2937
-
(2001)
J Chem Phys
, vol.114
, pp. 2924-2937
-
-
Im, W.1
Berneche, S.2
Roux, B.3
-
109
-
-
0002083815
-
Hybrid classical quantum force field for modelling very large molecules
-
Monard G, Loos M, Théry V, Baka K, Rivail J-L (1996) Hybrid classical quantum force field for modelling very large molecules. Int J Quantum Chem 58:153-159
-
(1996)
Int J Quantum Chem
, vol.58
, pp. 153-159
-
-
Monard, G.1
Loos, M.2
Théry, V.3
Baka, K.4
Rivail, J.-L.5
-
110
-
-
0030573150
-
Quantum chemical computations on parts of large molecules: The ab initio local self consistent field method
-
Assfeld X, Rivail J-L (1996) Quantum chemical computations on parts of large molecules: The ab initio local self consistent field method. Chem Phys Lett 263:100-106
-
(1996)
Chem Phys Lett
, vol.263
, pp. 100-106
-
-
Assfeld, X.1
Rivail, J.-L.2
-
111
-
-
0000411659
-
Method for the treatment of boundary atoms in combined qm/mm calculations
-
Gao J, Amara P, Alhambra C, Field MJ (1998) 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
-
112
-
-
0037197652
-
Specific force field parameters determination for the hybrid ab initio qm/mm lscf method
-
Ferre N, Assfeld X, Rivail J-L (2002) Specific force field parameters determination for the hybrid ab initio QM/MM LSCF method. J Comput Chem 23:610-624
-
(2002)
J Comput Chem
, vol.23
, pp. 610-624
-
-
Ferre, N.1
Assfeld, X.2
Rivail, J.-L.3
-
113
-
-
0032475433
-
Modeling of peptide hydrolysis by thermolysin. A semiempirical and qm/mm study
-
Antonczak S, Monard G, Ruiz-Lopez MF, Rivail J-L (1998) Modeling of Peptide Hydrolysis by Thermolysin. A Semiempirical and QM/MM Study. J Am Chem Soc 120:8825-8833
-
(1998)
J Am Chem Soc
, vol.120
, pp. 8825-8833
-
-
Antonczak, S.1
Monard, G.2
Ruiz-Lopez, M.F.3
Rivail, J.-L.4
-
114
-
-
2442538904
-
Generalized hybrid orbital for the treatment of boundary atoms in combined quantum mechanical and molecular mechanical calculations using the semiempirical parameterized model 3 method
-
Garcia-Viloca M, Gao JL (2004) Generalized hybrid orbital for the treatment of boundary atoms in combined quantum mechanical and molecular mechanical calculations using the semiempirical parameterized model 3 method. Theor Chem Acc 111:280-286
-
(2004)
Theor Chem Acc
, vol.111
, pp. 280-286
-
-
Garcia-Viloca, M.1
Gao, J.L.2
-
115
-
-
33750447832
-
Frozen density functional approach for ab-initio calculations of solvated molecules
-
Wesolowski TA, Warshel A (1993) Frozen density functional approach for ab-initio calculations of solvated molecules. J Phys Chem 97:8050-8053
-
(1993)
J Phys Chem
, vol.97
, pp. 8050-8053
-
-
Wesolowski, T.A.1
Warshel, A.2
-
116
-
-
0442279531
-
Generalized hybrid orbital (gho) method for combining ab initio hartree -fock wave functions with molecular mechanics
-
Pu JZ, Gao JL, Truhlar DG (2004) Generalized hybrid orbital (GHO) method for combining ab initio hartree -fock wave functions with molecular mechanics. J Phys Chem A 108:632-650
-
(2004)
J Phys Chem A
, vol.108
, pp. 632-650
-
-
Pu, J.Z.1
Gao, J.L.2
Truhlar, D.G.3
-
117
-
-
3142766126
-
Combining self-consistent-charge density-functional tight-binding (scc-dftb) with molecular mechanics by the generalized hybrid orbital (gho) method
-
Pu JZ, Gao JL, Truhlar DG (2004) Combining self-consistent-charge density-functional tight-binding (SCC-DFTB) with molecular mechanics by the generalized hybrid orbital (GHO) Method. J Phys Chem A 108:5454-5463
-
(2004)
J Phys Chem A
, vol.108
, pp. 5454-5463
-
-
Pu, J.Z.1
Gao, J.L.2
Truhlar, D.G.3
-
118
-
-
24944450993
-
Generalized hybrid-orbital method for combining density functional theory with molecular mechanicals
-
Pu JZ, Gao JL, Truhlar DG (2005) Generalized hybrid-orbital method for combining density functional theory with molecular mechanicals. Chemphyschem 6:1853-1865
-
(2005)
Chemphyschem
, vol.6
, pp. 1853-1865
-
-
Pu, J.Z.1
Gao, J.L.2
Truhlar, D.G.3
-
119
-
-
0037291485
-
Evaluation of an ab-initio quantum mechanical molecular mechanical hybrid-potential link-Atom method
-
Amara P, Field MJ (2003) Evaluation of an ab-initio quantum mechanical molecular mechanical hybrid-potential link-Atom method. Theor Chem Acc 109:43-52
-
(2003)
Theor Chem Acc
, vol.109
, pp. 43-52
-
-
Amara, P.1
Field, M.J.2
-
120
-
-
84892856784
-
-
Hyper Chem Users Manual Ontario, Canada
-
HyperChem Users Manual (2002) Hyper-Cube, Inc: Waterloo, Ontario, Canada
-
(2002)
Hyper-Cube Inc: Waterloo
-
-
-
121
-
-
0001763714
-
Frontier bonds in qm/mm methods: A comparison of different approaches
-
Reuter N, Dejaegere A, Maigret B, KarplusM (2000) Frontier bonds in QM/MM methods: a comparison of different approaches. J Phys Chem A 104:1720-1735
-
(2000)
J Phys Chem A
, vol.104
, pp. 1720-1735
-
-
Reuter, N.1
Dejaegere, A.2
Maigret, B.3
Karplus, M.4
-
122
-
-
0001582558
-
A pseudobond approach to combining quantum mechanical and molecular mechanical methods
-
Zhang Y, Lee T-S, Yang W (1999) A pseudobond approach to combining quantum mechanical and molecular mechanical methods. J Chem Phys 110:46-54
-
(1999)
J Chem Phys
, vol.110
, pp. 46-54
-
-
Zhang, Y.1
Lee, T.-S.2
Yang, W.3
-
124
-
-
0037115887
-
Optimization of quantum mechanical molecular mechanical partitioning schemes: Gaussian delocalization of molecular mechanical charges and the double link atom method
-
Das D, Eurenius KP, Billings EM, Sherwood P, Chatfield DC, Hodoscek M, Brooks BR (2002) Optimization of quantum mechanical molecular mechanical partitioning schemes: Gaussian delocalization of molecular mechanical charges and the double link atom method. J Chem Phys 117:10534-10547
-
(2002)
J Chem Phys
, vol.117
, pp. 10534-10547
-
-
Das, D.1
Eurenius, K.P.2
Billings, E.M.3
Sherwood, P.4
Chatfield, D.C.5
Hodoscek, M.6
Brooks, B.R.7
-
125
-
-
19944408652
-
A critical evaluation of different qm/mm frontier treatments with sccdftb as the qm method
-
Konig PH, Hoffmann M, Frauenheim T, Cui Q (2005) A critical evaluation of different QM/MM frontier treatments with SCCDFTB as the QM method. J Phys Chem B 109:9082-9095
-
(2005)
J Phys Chem B
, vol.109
, pp. 9082-9095
-
-
Konig, P.H.1
Hoffmann, M.2
Frauenheim, T.3
Cui, Q.4
-
126
-
-
24344484047
-
On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions
-
Klahn M, Braun-Sand S, Rosta E, Warshel A (2005) On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions. J Phys Chem B 109:15645-15650
-
(2005)
J Phys Chem B
, vol.109
, pp. 15645-15650
-
-
Klahn, M.1
Braun-Sand, S.2
Rosta, E.3
Warshel, A.4
-
127
-
-
77956595530
-
Structural fluctuations in enzyme-catalyzed reactions: Determinants of reactivity in fatty acid amide hydrolase from multivariate statistical analysis of quantum mechanics/molecular mechanics paths
-
Lodola A, Sirirak J, Fey N, Rivara S, Mor M, Mulholland AJ (2010) Structural fluctuations in enzyme-catalyzed reactions: determinants of reactivity in fatty acid amide hydrolase from multivariate statistical analysis of quantum mechanics/molecular mechanics paths. J Chem Theor Comput 6:2948-2960
-
(2010)
J Chem Theor Comput
, vol.6
, pp. 2948-2960
-
-
Lodola, A.1
Sirirak, J.2
Fey, N.3
Rivara, S.4
Mor, M.5
Mulholland, A.J.6
-
128
-
-
34249680791
-
Molecular determinants of xenobiotic metabolism: Qm/mm simulation of the conversion of 1-chloro-2,4-dinitrobenzene catalyzed by m1-1 glutathione s-transferase
-
Bowman AL, Ridder L, Rietjens IMCM, Vervoort J, Mulholland AJ (2007) Molecular determinants of xenobiotic metabolism: QM/MM simulation of the conversion of 1-chloro-2,4-dinitrobenzene catalyzed by M1-1 glutathione S-transferase. Biochemistry 46:6353-6363
-
(2007)
Biochemistry
, vol.46
, pp. 6353-6363
-
-
Bowman, A.L.1
Ridder, L.2
Imcm, R.3
Vervoort, J.4
Mulholland, A.J.5
-
129
-
-
75449116384
-
Advances in quantum and molecular mechanical (qm/mm) simulations for organic and enzymatic reactions
-
Acevedo O, Jorgensen WL (2010) Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions. Acc Chem Res 43:142-151
-
(2010)
Acc Chem Res
, vol.43
, pp. 142-151
-
-
Acevedo, O.1
Jorgensen, W.L.2
-
130
-
-
38049039241
-
An efficient method for the calculation of quantum mechanics/molecular mechanics free energies
-
Art. No 014109
-
Woods CJ, Manby FR, Mulholland AJ (2008) An efficient method for the calculation of quantum mechanics/molecular mechanics free energies. J Chem Phys 128:Art. No. 014109
-
(2008)
J Chem Phys
, vol.128
-
-
Woods, C.J.1
Manby, F.R.2
Mulholland, A.J.3
-
131
-
-
0141499408
-
Modeling biotransformation reactions by combined quantum mechanical/molecular mechanical approaches: From structure to activity
-
Ridder L, Mulholland AJ (2003) Modeling biotransformation reactions by combined quantum mechanical/molecular mechanical approaches: from structure to activity. Curr Top Med Chem 3:1241-1256
-
(2003)
Curr Top Med Chem
, vol.3
, pp. 1241-1256
-
-
Ridder, L.1
Mulholland, A.J.2
-
132
-
-
77956092555
-
Testing highlevel qm/mm methods for modeling enzyme reactions: Acetyl-coa deprotonation in citrate synthase
-
van der Kamp MW, Zurek J, Manby FR, Harvey JN, Mulholland AJ (2010) Testing highlevel QM/MM methods for modeling enzyme reactions: acetyl-CoA deprotonation in citrate synthase. J Phys Chem B 114:11303-11314
-
(2010)
J Phys Chem B
, vol.114
, pp. 11303-11314
-
-
Van Der Kamp, M.W.1
Zurek, J.2
Manby, F.R.3
Harvey, J.N.4
Mulholland, A.J.5
-
133
-
-
34548435241
-
Analysis of classical and quantum paths for deprotonation of methylamine by methylamine dehydrogenase
-
Ranaghan KE, Masgrau L, Scrutton NS, Sutcliffe MJ, Mulholland AJ (2007) Analysis of classical and quantum paths for deprotonation of methylamine by methylamine dehydrogenase. Chemphyschem 8:1816-1835
-
(2007)
Chemphyschem
, vol.8
, pp. 1816-1835
-
-
Ranaghan, K.E.1
Masgrau, L.2
Scrutton, N.S.3
Sutcliffe, M.J.4
Mulholland, A.J.5
|