-
1
-
-
2142746284
-
The activated complex in chemical reactions
-
H. Eyring The activated complex in chemical reactions J. Chem. Phys. 3 1935 107 115
-
(1935)
J. Chem. Phys.
, vol.3
, pp. 107-115
-
-
Eyring, H.1
-
2
-
-
0042061008
-
Exploring potential energy surfaces for chemical reactions: An overview of some practical methods
-
H.B. Schlegel Exploring potential energy surfaces for chemical reactions: an overview of some practical methods J. Comput. Chem. 24 2003 1514 1527
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1514-1527
-
-
Schlegel, H.B.1
-
3
-
-
84987058840
-
Self-avoiding walk between two fixed points as a tool to calculate reaction paths in large molecular systems
-
R. Czermiński, and R. Elber Self-avoiding walk between two fixed points as a tool to calculate reaction paths in large molecular systems Int. J. Quantum Chem.: Quantum Chem. Symp. 24 1990 167 186
-
(1990)
Int. J. Quantum Chem.: Quantum Chem. Symp.
, vol.24
, pp. 167-186
-
-
Czermiński, R.1
Elber, R.2
-
4
-
-
0011690680
-
Methods for finding saddle points and minimum energy paths
-
S.D. Schwartz Kluwer Academic Publishers
-
G. Henkelman, G. Jóhannesson, and H. Jónsson Methods for finding saddle points and minimum energy paths S.D. Schwartz Theoretical Methods in Condensed Phase Chemistry, Vol. 5, Progress on Theoretical Chemistry and Physics 2000 Kluwer Academic Publishers 269 300
-
(2000)
Theoretical Methods in Condensed Phase Chemistry, Vol. 5, Progress on Theoretical Chemistry and Physics
, pp. 269-300
-
-
Henkelman, G.1
Jóhannesson, G.2
Jónsson, H.3
-
5
-
-
0000220710
-
Nudged elastic band method for finding minimum energy paths of transitions
-
B.J. Berne G. Ciccotti D.F. Coker World Scientific Singapore
-
H. Jónsson, G. Mills, and K.W. Jacobsen Nudged elastic band method for finding minimum energy paths of transitions B.J. Berne G. Ciccotti D.F. Coker Classical and quantum dynamics in condensed phase simulations 1998 World Scientific Singapore 385 404
-
(1998)
Classical and Quantum Dynamics in Condensed Phase Simulations
, pp. 385-404
-
-
Jónsson, H.1
Mills, G.2
Jacobsen, K.W.3
-
8
-
-
0002531265
-
Methods for calculation of free energies and binding constants: Successes and problems
-
W.F. van Gunsteren P.K. Weiner ESCOM Science Publishers B.V. The Netherlands
-
W.F. van Gunsteren Methods for calculation of free energies and binding constants: successes and problems W.F. van Gunsteren P.K. Weiner Computer simulation of biomolecular systems: theoretical and experimental applications 1989 ESCOM Science Publishers B.V. The Netherlands 27 59
-
(1989)
Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications
, pp. 27-59
-
-
Van Gunsteren, W.F.1
-
9
-
-
0035799954
-
First-principle molecular dynamic simulations along the intrinsic reaction paths
-
A. Michalak, and T. Ziegler First-principle molecular dynamic simulations along the intrinsic reaction paths J. Phys. Chem. A 105 2001 4333 4343
-
(2001)
J. Phys. Chem. A
, vol.105
, pp. 4333-4343
-
-
Michalak, A.1
Ziegler, T.2
-
10
-
-
0037164091
-
Reaction Mechanism of the HGXPRTase from Plasmodium flaciparum: A hybrid potential quantum mechanical/molecular mechanical study
-
A. Thomas, and M.J. Field Reaction Mechanism of the HGXPRTase from Plasmodium flaciparum: a hybrid potential quantum mechanical/molecular mechanical study J. Am. Chem. Soc. 124 42 2002 12432 12438
-
(2002)
J. Am. Chem. Soc.
, vol.124
, Issue.42
, pp. 12432-12438
-
-
Thomas, A.1
Field, M.J.2
-
11
-
-
0019748203
-
Structural features of the phosphoribosyltransferases and their relationship to the human deficiency disorders of purine and pyrimidine metabolism
-
W.D.L. Musick Structural features of the phosphoribosyltransferases and their relationship to the human deficiency disorders of purine and pyrimidine metabolism CRC Crit. Rev. Biochem. X 1981 1 34
-
(1981)
CRC Crit. Rev. Biochem.
, vol.10
, pp. 1-34
-
-
Musick, W.D.L.1
-
12
-
-
0034617303
-
Purine phosphoribosyltransferases III
-
S.P. Craig, A.E. Eakin, and Purine phosphoribosyltransferases III J. Biol. Chem. 275 2000 20231 20234
-
(2000)
J. Biol. Chem.
, vol.275
, pp. 20231-20234
-
-
Craig, S.P.1
Eakin, A.E.2
-
13
-
-
0000831054
-
The Dynamo library for molecular simulations using hybrid quantum mechanical and molecular mechanical Potentials
-
M.J. Field, M. Albe, C. Bret, F. Proust-de Martin, and A. Thomas The Dynamo library for molecular simulations using hybrid quantum mechanical and molecular mechanical Potentials J. Comput. Chem. 21 2000 1088 1100
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 1088-1100
-
-
Field, M.J.1
Albe, M.2
Bret, C.3
Proust-De Martin, F.4
Thomas, A.5
-
14
-
-
0000519270
-
Combined quantum mechanical and molecular mechanical potentials
-
P. Kollman N. Allinger Wiley
-
P. Amara, and M.J. Field Combined quantum mechanical and molecular mechanical potentials P. Kollman N. Allinger Encyclopedia of Computational Chemistry 1998 Wiley 179 183
-
(1998)
Encyclopedia of Computational Chemistry
, pp. 179-183
-
-
Amara, P.1
Field, M.J.2
-
15
-
-
0012576082
-
Hybrid quantum mechanics/molecular mechanics approaches
-
Johannes Grotendorst, (Ed.), NIC series, John von Neumann Institute for Computing, Jülich
-
P. Sherwood, Hybrid quantum mechanics/molecular mechanics approaches, in: Johannes Grotendorst, (Ed.), Modern Methods and Algorithms of Quantum Chemistry Proceedings, second ed., NIC series, John von Neumann Institute for Computing, Jülich, 2000. pp. 285-305.
-
(2000)
Modern Methods and Algorithms of Quantum Chemistry Proceedings, Second Ed.
, pp. 285-305
-
-
Sherwood, P.1
-
16
-
-
0034705109
-
Reaction coordinates of biomolecular isomerization
-
P.G. Bolhuis, C. Dellago, and D. Chandler Reaction coordinates of biomolecular isomerization Proc. Natl. Acad. Sci. 97 11 2000 5877 5882
-
(2000)
Proc. Natl. Acad. Sci.
, vol.97
, Issue.11
, pp. 5877-5882
-
-
Bolhuis, P.G.1
Dellago, C.2
Chandler, D.3
-
17
-
-
0001568871
-
Calculation of conformational transitions and barriers in solvated systems: Application to the alanine dipeptide in water
-
J. Apostolakis, P. Ferrara, and A. Caflisch Calculation of conformational transitions and barriers in solvated systems: application to the alanine dipeptide in water J. Chem. Phys. 110 4 1999 2099 2108
-
(1999)
J. Chem. Phys.
, vol.110
, Issue.4
, pp. 2099-2108
-
-
Apostolakis, J.1
Ferrara, P.2
Caflisch, A.3
-
18
-
-
0029912748
-
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
-
W.L. Jorgensen, D.S. Maxwell, and J. Tirado-Rives Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids J. Am. Chem. Soc. 118 1996 11225 11236
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
19
-
-
0033519996
-
The 2.0 Å structure of malarial purine phosphoribosyltransferase in complex with a transition-state analogue inhibitor
-
W. Shi, C.M. Li, P.C. Tyler, R.H. Furneaux, S.M. Cahill, M.E. Girvin, C. Grubmeyer, V.L. Schramm, and S.C. Almo The 2.0 Å structure of malarial purine phosphoribosyltransferase in complex with a transition-state analogue inhibitor Biochemistry 38 1999 9872 9880
-
(1999)
Biochemistry
, vol.38
, pp. 9872-9880
-
-
Shi, W.1
Li, C.M.2
Tyler, P.C.3
Furneaux, R.H.4
Cahill, S.M.5
Girvin, M.E.6
Grubmeyer, C.7
Schramm, V.L.8
Almo, S.C.9
-
20
-
-
0034483903
-
Substrate deformation in a hypoxanthine-guanine phosphoribosyltransferase ternary complex: The structural basis for catalysis
-
A. Heroux, E.L. White, L.J. Ross, A.P. Kuzin, and D.W. Borhani Substrate deformation in a hypoxanthine-guanine phosphoribosyltransferase ternary complex: the structural basis for catalysis Struct. Fold Des. 8 12 2000 1309 1318
-
(2000)
Struct. Fold Des.
, vol.8
, Issue.12
, pp. 1309-1318
-
-
Heroux, A.1
White, E.L.2
Ross, L.J.3
Kuzin, A.P.4
Borhani, D.W.5
-
22
-
-
1442282189
-
A doubly nudged elastic band method for finding transition states
-
S.A. Trygubenko, and D.J. Wales A doubly nudged elastic band method for finding transition states J. Chem. Phys. 120 2004 2082 2094
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 2082-2094
-
-
Trygubenko, S.A.1
Wales, D.J.2
-
23
-
-
0942268404
-
A super-linear minimization scheme for the nudged elastic band method
-
J.-W. Chu, B.L. Trout, and B. Brooks A super-linear minimization scheme for the nudged elastic band method J. Chem. Phys. 119 24 2003 12708 12717
-
(2003)
J. Chem. Phys.
, vol.119
, Issue.24
, pp. 12708-12717
-
-
Chu, J.-W.1
Trout, B.L.2
Brooks, B.3
-
25
-
-
1242329035
-
Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points
-
G. Henkelman, and H. Jónsson Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points J. Chem. Phys. 113 2000 9978 9985
-
(2000)
J. Chem. Phys.
, vol.113
, pp. 9978-9985
-
-
Henkelman, G.1
Jónsson, H.2
-
26
-
-
2442486484
-
A growing string method for determining transition states: Comparison to the nudged elastic band and string methods
-
B. Peters, A. Heyden, A.T. Bell, and A. Chakraborty A growing string method for determining transition states: comparison to the nudged elastic band and string methods J. Chem. Phys. 120 2004 7877 7886
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 7877-7886
-
-
Peters, B.1
Heyden, A.2
Bell, A.T.3
Chakraborty, A.4
-
27
-
-
0037044123
-
Adaptive nudged elastic band approach for transition state calculation
-
P. Maragakis, S.A. Andreev, Y. Brumer, D.R. Reichman, and E. Kaxiras Adaptive nudged elastic band approach for transition state calculation J. Chem. Phys. 117 10 2002 4651 4657
-
(2002)
J. Chem. Phys.
, vol.117
, Issue.10
, pp. 4651-4657
-
-
Maragakis, P.1
Andreev, S.A.2
Brumer, Y.3
Reichman, D.R.4
Kaxiras, E.5
-
28
-
-
2442573648
-
Adapting the nudged elastic band method for determining minimum energy paths of chemical reactions in enzymes
-
L. Xie, H. Liu, and W. Yang Adapting the nudged elastic band method for determining minimum energy paths of chemical reactions in enzymes J. Chem. Phys. 120 2004 8039 8052
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 8039-8052
-
-
Xie, L.1
Liu, H.2
Yang, W.3
-
29
-
-
0003067207
-
Location of saddle points and minimum energy paths by a constrained simplex optimization procedure
-
K. Müller, and L.D. Brown Location of saddle points and minimum energy paths by a constrained simplex optimization procedure Theor. Chim. Acta 53 1979 75 93
-
(1979)
Theor. Chim. Acta
, vol.53
, pp. 75-93
-
-
Müller, K.1
Brown, L.D.2
-
30
-
-
0035695812
-
Atomic motion in enzymatic reaction coordinates
-
V.L. Schramm, and W. Shi Atomic motion in enzymatic reaction coordinates Curr. Op. Struct. Biol. 11 2001 657 665
-
(2001)
Curr. Op. Struct. Biol.
, vol.11
, pp. 657-665
-
-
Schramm, V.L.1
Shi, W.2
-
31
-
-
0000055722
-
Diffusion-controlled reactions: A variational formula for the optimum reaction coordinate
-
M. Berkowitz, J.D. Morgan, J.D. McCammon, and S.H. Northrup Diffusion-controlled reactions: a variational formula for the optimum reaction coordinate J. Chem. Phys. 79 1983 5563 5565
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 5563-5565
-
-
Berkowitz, M.1
Morgan, J.D.2
McCammon, J.D.3
Northrup, S.H.4
-
32
-
-
0031256658
-
The Max Flux algorithm for calculating variationally optimized reaction paths for conformational transitions in many body systems at a finite temperature
-
S. Huo, and J.E. Straub The Max Flux algorithm for calculating variationally optimized reaction paths for conformational transitions in many body systems at a finite temperature J. Chem. Phys. 107 1997 5000 5006
-
(1997)
J. Chem. Phys.
, vol.107
, pp. 5000-5006
-
-
Huo, S.1
Straub, J.E.2
-
33
-
-
0038340986
-
A temperature-dependent nudged-elastic-band algorithm
-
R. Crehuet, and M.J. Field A temperature-dependent nudged-elastic-band algorithm J. Chem. Phys. 118 2003 9563 9571
-
(2003)
J. Chem. Phys.
, vol.118
, pp. 9563-9571
-
-
Crehuet, R.1
Field, M.J.2
|