-
3
-
-
0013890240
-
-
Warren, S.; Zerner, B.; Westheimer, F. H. Biochemistry 1966, 5, 817.
-
(1966)
Biochemistry
, vol.5
, pp. 817
-
-
Warren, S.1
Zerner, B.2
Westheimer, F.H.3
-
6
-
-
0025775806
-
-
Smiley, J. A.; Paneth, M. H.; O'Leary, M. H.; Bell, J. B.; Jones, M. E. Biochemistry 1991, 30, 6216.
-
(1991)
Biochemistry
, vol.30
, pp. 6216
-
-
Smiley, J.A.1
Paneth, M.H.2
O'Leary, M.H.3
Bell, J.B.4
Jones, M.E.5
-
8
-
-
58149226532
-
-
Houk, K. N.; Tantillo, D. J.; Stanton, C.; Hu, Y. Top. Curr. Chem. 2004, 258, 1.
-
(2004)
Top. Curr. Chem
, vol.258
, pp. 1
-
-
Houk, K.N.1
Tantillo, D.J.2
Stanton, C.3
Hu, Y.4
-
12
-
-
0034639902
-
-
Singleton, D. A.; Merrigan, S. R.; Kim, B. J.; Beak, P.; Phillips, L. M.; Lee, J. K. J. Am. Chem. Soc. 2000, 122, 3296.
-
(2000)
J. Am. Chem. Soc
, vol.122
, pp. 3296
-
-
Singleton, D.A.1
Merrigan, S.R.2
Kim, B.J.3
Beak, P.4
Phillips, L.M.5
Lee, J.K.6
-
13
-
-
0035793646
-
-
Houk, K. N.; Lee, J. K.; Tantillo, D. J.; Bahmanyar, S.; Hietbrink, B. N. ChemBioChem 2001, 2, 113.
-
(2001)
ChemBioChem
, vol.2
, pp. 113
-
-
Houk, K.N.1
Lee, J.K.2
Tantillo, D.J.3
Bahmanyar, S.4
Hietbrink, B.N.5
-
14
-
-
0035956573
-
-
Lee, T. S.; Chong, L. T.; Chodera, J. D.; Kollman, P. J. Am. Chem. Soc. 2001, 123, 12837.
-
(2001)
J. Am. Chem. Soc
, vol.123
, pp. 12837
-
-
Lee, T.S.1
Chong, L.T.2
Chodera, J.D.3
Kollman, P.4
-
17
-
-
0034058368
-
-
Appleby, T. C.; Kinsland, C.; Begley, T. P.; Ealick, S. E. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 2005.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A
, vol.2000
, pp. 97
-
-
Appleby, T.C.1
Kinsland, C.2
Begley, T.P.3
Ealick, S.E.4
-
18
-
-
0034104285
-
-
Miller, B. G.; Hassell, A. M.; Wolfenden, R.; Milburn, M. V.; Short, S. A. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 2011.
-
(2000)
Proc. Natl. Acad. Sci. U.S.A
, vol.97
, pp. 2011
-
-
Miller, B.G.1
Hassell, A.M.2
Wolfenden, R.3
Milburn, M.V.4
Short, S.A.5
-
19
-
-
0034681950
-
-
Harris, P.; Poulsen, J.-C. N.; Jense, K. F.; Larsen, S. Biochemistry 2000, 39, 4217.
-
(2000)
Biochemistry
, vol.39
, pp. 4217
-
-
Harris, P.1
Poulsen, J.-C.N.2
Jense, K.F.3
Larsen, S.4
-
20
-
-
0034102419
-
-
Wu, N.; Mo, Y.; Gao, J.; Pai, E. F. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 2017.
-
(2000)
Proc. Natl. Acad. Sci. U.S.A
, vol.97
, pp. 2017
-
-
Wu, N.1
Mo, Y.2
Gao, J.3
Pai, E.F.4
-
21
-
-
0019334745
-
-
Levine, H. L.; Brody, R. S.; Westheimer, F. H. Biochemistry 1980, 19, 4993.
-
(1980)
Biochemistry
, vol.19
, pp. 4993
-
-
Levine, H.L.1
Brody, R.S.2
Westheimer, F.H.3
-
23
-
-
0034610398
-
-
Warshel, A.; Štrajbl, M.; Villà, J.; Florián, J. Biochemistry 2000, 39, 14728.
-
(2000)
Biochemistry
, vol.39
, pp. 14728
-
-
Warshel, A.1
Štrajbl, M.2
Villà, J.3
Florián, J.4
-
24
-
-
0035793649
-
-
Warshel, A.; Florián, J.; Štrajbl, M.; Villà, J. ChemBioChem 2001, 2, 109.
-
(2001)
ChemBioChem
, vol.2
, pp. 109
-
-
Warshel, A.1
Florián, J.2
Štrajbl, M.3
Villà, J.4
-
25
-
-
33846255198
-
-
Lundberg, M.; Blomberg, M. R. A.; Siegbahn, P. E. M. Top. Curr. Chem. 2004, 238, 79.
-
(2004)
Top. Curr. Chem
, vol.238
, pp. 79
-
-
Lundberg, M.1
Blomberg, M.R.A.2
Siegbahn, P.E.M.3
-
26
-
-
10044248161
-
-
Raugei, S.; Cascella, M.; Carloni, P. J. Am. Chem. Soc. 2004, 126, 15730.
-
(2004)
J. Am. Chem. Soc
, vol.126
, pp. 15730
-
-
Raugei, S.1
Cascella, M.2
Carloni, P.3
-
27
-
-
84906377330
-
-
Cascella, M.; Guidoni, L.; Rothlisberger, U.; Maritan, A.; Carloni, P. J. Phys. Chem. B 2002, 106, 13207.
-
(2002)
J. Phys. Chem. B
, vol.106
, pp. 13207
-
-
Cascella, M.1
Guidoni, L.2
Rothlisberger, U.3
Maritan, A.4
Carloni, P.5
-
29
-
-
0034058368
-
-
Appleby, T. C.; Kinsland, C.; Begley, T. P.; Ealick, S. E. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 2005.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A
, vol.2000
, pp. 97
-
-
Appleby, T.C.1
Kinsland, C.2
Begley, T.P.3
Ealick, S.E.4
-
30
-
-
84906414178
-
-
Reference deleted in proof
-
Reference deleted in proof.
-
-
-
-
32
-
-
2942548219
-
-
Micheletti, C.; Laio, A.; Parrinello, M. Phys. Rev. Lett. 2004, 92, 170601.
-
(2004)
Phys. Rev. Lett
, vol.92
, pp. 170601
-
-
Micheletti, C.1
Laio, A.2
Parrinello, M.3
-
33
-
-
84906385292
-
-
For more information on CP2K, see: http://cp2k.berlios.de/.
-
For more information on CP2K, see: http://cp2k.berlios.de/.
-
-
-
-
34
-
-
15344345714
-
-
VandeVondele, J.; Krack, M.; Mohamed, F.; Parrinello, M.; Chassaing, T.; Hutter, J. Comput. Phys. Commun. 2005, 167, 103.
-
(2005)
Comput. Phys. Commun
, vol.167
, pp. 103
-
-
VandeVondele, J.1
Krack, M.2
Mohamed, F.3
Parrinello, M.4
Chassaing, T.5
Hutter, J.6
-
35
-
-
0039209924
-
-
Schaefer, A.; Huber, C.; Ahlrichs, R. J. Chem. Phys. 1994, 100, 5829.
-
(1994)
J. Chem. Phys
, vol.100
, pp. 5829
-
-
Schaefer, A.1
Huber, C.2
Ahlrichs, R.3
-
36
-
-
0000160164
-
-
Goedecker, S.; Teter, M.; Hutter, J. Phys. Rev. B 1996, 54, 1703.
-
(1996)
Phys. Rev. B
, vol.54
, pp. 1703
-
-
Goedecker, S.1
Teter, M.2
Hutter, J.3
-
37
-
-
0000083717
-
-
Hartwigsen, C.; Goedecker, S.; Hutter, J. Phys. Rev. B 1998, 58, 3641.
-
(1998)
Phys. Rev. B
, vol.58
, pp. 3641
-
-
Hartwigsen, C.1
Goedecker, S.2
Hutter, J.3
-
39
-
-
0345491105
-
-
Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785.
-
(1988)
Phys. Rev. B
, vol.37
, pp. 785
-
-
Lee, C.1
Yang, W.2
Parr, R.G.3
-
40
-
-
84906399779
-
-
MacKerell, A. D., Jr.; Brooks, B.; Brooks, C. L., III; Nilsson, L.; Roux, B.; Won, Y.; Karplus M. In The Encyclopedia of Computational Chemistry, 1; Schleyer, P. v. R., et al., Ed.; John Wiley & Sons: Chichester, U.K., 1998; pp 271-277,.
-
MacKerell, A. D., Jr.; Brooks, B.; Brooks, C. L., III; Nilsson, L.; Roux, B.; Won, Y.; Karplus M. In The Encyclopedia of Computational Chemistry, Vol. 1; Schleyer, P. v. R., et al., Ed.; John Wiley & Sons: Chichester, U.K., 1998; pp 271-277,.
-
-
-
-
42
-
-
33646205963
-
-
Laino, T.; Mohamed, F.; Laio, A.; Parrinello, M. J. Chem. Theory Comput. 2005, 1, 1176.
-
(2005)
Chem. Theory Comput
, vol.1
, pp. 1176
-
-
Laino, T.1
Mohamed, F.2
Laio, A.3
Parrinello, M.J.4
-
44
-
-
33746228476
-
-
Gervasio, F. L.; Parrinello, M.; Ceccarelli, M.; Klein, M. L. J. Mol. Biol. 2006, 361, 390.
-
(2006)
J. Mol. Biol
, vol.361
, pp. 390
-
-
Gervasio, F.L.1
Parrinello, M.2
Ceccarelli, M.3
Klein, M.L.4
-
45
-
-
33644752094
-
-
Lee, J. G.; Asciutto, E.; Babin, V.; Sagui, C.; Darden, T.; Roland, C. J. Phys. Chem. B 2006, 110, 2325.
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 2325
-
-
Lee, J.G.1
Asciutto, E.2
Babin, V.3
Sagui, C.4
Darden, T.5
Roland, C.6
-
46
-
-
14744276066
-
-
Gervasio, F. L.; Laio, A.; Parrinello, M. J. Am. Chem. Soc. 2005, 127, 2600.
-
(2005)
J. Am. Chem. Soc
, vol.127
, pp. 2600
-
-
Gervasio, F.L.1
Laio, A.2
Parrinello, M.3
-
47
-
-
17444412296
-
-
Laio, A.; Rodriguez-Fortes, A.; Gervasio, F. L.; Ceccarelli, M.; Parrinello, M. /. Phys. Chem. B 2005, 109, 6714.
-
(2005)
Phys. Chem. B
, vol.109
, pp. 6714
-
-
Laio, A.1
Rodriguez-Fortes, A.2
Gervasio, F.L.3
Ceccarelli, M.4
Parrinello, M.5
-
48
-
-
84906370932
-
-
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.; Pople, J. A. Gaussian 03, Revision D.01; Gaussian, Inc.: Wallingford, CT, 2004.
-
-
-
-
50
-
-
84906385293
-
-
Deleted at proof
-
Deleted at proof.
-
-
-
-
51
-
-
0006012501
-
-
Montgomery, J. A., Jr.; Frisch, M. J.; Ochterski, J. W.; Petersson, G. A. J. Chem. Phys. 2000, 112, 6532.
-
(2000)
J. Chem. Phys
, vol.112
, pp. 6532
-
-
Montgomery Jr., J.A.1
Frisch, M.J.2
Ochterski, J.W.3
Petersson, G.A.4
-
52
-
-
0000340764
-
-
Montgomery, J. A., Jr.; Frisch, M. J.; Ochterski, J. W.; Petersson, G. A. J. Chem. Phys. 1999, 110, 2822.
-
(1999)
J. Chem. Phys
, vol.110
, pp. 2822
-
-
Montgomery Jr., J.A.1
Frisch, M.J.2
Ochterski, J.W.3
Petersson, G.A.4
-
53
-
-
0029962912
-
-
Yablonski, M. J.; Pasek, D. A.; Han, B. D.; Jones, M. E.; Traut, T. W. J. Biol. Chem. 1996, 271, 10704.
-
(1996)
J. Biol. Chem
, vol.271
, pp. 10704
-
-
Yablonski, M.J.1
Pasek, D.A.2
Han, B.D.3
Jones, M.E.4
Traut, T.W.5
-
55
-
-
27344436659
-
-
Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kale, L.; Schulten, K. J. Comput. Chem. 2005, 26, 1781.
-
(2005)
J. Comput. Chem
, vol.26
, pp. 1781
-
-
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
-
56
-
-
0035892208
-
-
Pokon, E. K.; Liptak, M. D.; Feldgus, S.; Shields, G. C. J. Phys. Chem. A 2001, 105, 10483.
-
(2001)
J. Phys. Chem. A
, vol.105
, pp. 10483
-
-
Pokon, E.K.1
Liptak, M.D.2
Feldgus, S.3
Shields, G.C.4
-
57
-
-
0029878720
-
-
Humphrey, W.; Dalke, A.; Schulten, K. J. Mol. Graphics 1996, 14, 33.
-
(1996)
J. Mol. Graphics
, vol.14
, pp. 33
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
58
-
-
84906370933
-
-
2 of the amide side chain forms hydrogen bonds with the phosphate group and O2 of BMP. The reference for the crystal structure (ref 13) describes a hydrogen bond between Gln215 and BMP at O2. It is likely there is a mistake in the PDB file, and the positions of the N and O of the amide should be reversed.
-
2 of the amide side chain forms hydrogen bonds with the phosphate group and O2 of BMP. The reference for the crystal structure (ref 13) describes a hydrogen bond between Gln215 and BMP at O2. It is likely there is a mistake in the PDB file, and the positions of the N and O of the amide should be reversed.
-
-
-
-
59
-
-
84906414176
-
-
The heavy atom distances are 3.76 and 2.66 Å in the crystal structure and simulation, respectively.
-
The heavy atom distances are 3.76 and 2.66 Å in the crystal structure and simulation, respectively.
-
-
-
-
60
-
-
84906385287
-
-
The heavy atom distances are 2.76 and 4.20 Å in the crystal structure and simulation, respectively.
-
The heavy atom distances are 2.76 and 4.20 Å in the crystal structure and simulation, respectively.
-
-
-
-
61
-
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84906385288
-
-
The heavy atom distances are 3.17 and 5.74 Å in the crystal structure and simulation, respectively.
-
The heavy atom distances are 3.17 and 5.74 Å in the crystal structure and simulation, respectively.
-
-
-
-
62
-
-
33644968698
-
-
Ensing, B.; Vivo, M. D.; Liu, Z.; Moore, P.; Klein, M. Acc. Chem. Res. 2006, 39, 73.
-
(2006)
Acc. Chem. Res
, vol.39
, pp. 73
-
-
Ensing, B.1
Vivo, M.D.2
Liu, Z.3
Moore, P.4
Klein, M.5
-
63
-
-
84906385289
-
-
The heavy atom distances are 2.92 and 3.20 Å in the large and small QM TS structures, respectively.
-
The heavy atom distances are 2.92 and 3.20 Å in the large and small QM TS structures, respectively.
-
-
-
-
65
-
-
84906414177
-
-
uncat.
-
uncat.
-
-
-
-
67
-
-
0042852135
-
-
Gullingsrud, J. R.; Braun, R.; Chulten, K. J. Comput. Phys. 1999, 151, 190.
-
(1999)
J. Comput. Phys
, vol.151
, pp. 190
-
-
Gullingsrud, J.R.1
Braun, R.2
Chulten, K.3
-
68
-
-
0029912748
-
-
Jorgensen, W. I.; Maxwell, D. S.; Tirado-Rives, J. J. Am. Chem. Soc. 1996, 118, 11225.
-
(1996)
J. Am. Chem. Soc
, vol.118
, pp. 11225
-
-
Jorgensen, W.I.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
69
-
-
0037149142
-
-
Lennartz, C.; Schäfer, A.; Terstegen, F.; Thiel, W. J. Phys. Chem. B 2002, 106, 1758.
-
(2002)
J. Phys. Chem. B
, vol.106
, pp. 1758
-
-
Lennartz, C.1
Schäfer, A.2
Terstegen, F.3
Thiel, W.4
-
70
-
-
0141727339
-
-
Loeffer, H. H.; Mohammed, A. M.; Inada, Y.; Funahashi, S. Chem. Phys. Lett. 2003, 379, 452.
-
(2003)
Chem. Phys. Lett
, vol.379
, pp. 452
-
-
Loeffer, H.H.1
Mohammed, A.M.2
Inada, Y.3
Funahashi, S.4
-
71
-
-
25144520939
-
-
Bathelt, C. M.; Zurek, J.; Mulholland, A. J.; Harvey, J. N. J. Am. Chem. Soc. 2005, 127, 12900.
-
(2005)
J. Am. Chem. Soc
, vol.127
, pp. 12900
-
-
Bathelt, C.M.1
Zurek, J.2
Mulholland, A.J.3
Harvey, J.N.4
-
72
-
-
0003544049
-
-
BIOMOS b.v: Zürich, Switzerland, Groningen, Germany
-
van Gunsteren, W. F.; Billeter, S. R.; Eising, A. A.; Hünenberger, P. H.; Krüger, P.; Mark, A. E.; Scott, W. R. P.; Tironi, I. G. Biomolecular simulation: GROMOS96 manual and user guide; BIOMOS b.v: Zürich, Switzerland, Groningen, Germany, 1996.
-
(1996)
Biomolecular simulation: GROMOS96 manual and user guide
-
-
van Gunsteren, W.F.1
Billeter, S.R.2
Eising, A.A.3
Hünenberger, P.H.4
Krüger, P.5
Mark, A.E.6
Scott, W.R.P.7
Tironi, I.G.8
-
73
-
-
84962448531
-
-
Donnini, S.; Groenhof, G.; Wierenga, R. K.; Juffer, A. H. Prot Struct. Funct. Bioinf. 2006, 64, 700.
-
(2006)
Struct. Funct. Bioinf
, vol.64
, pp. 700
-
-
Donnini, S.1
Groenhof, G.2
Wierenga, R.K.3
|