-
1
-
-
34250782571
-
Minimalist active-site redesign: Teaching old enzymes new tricks
-
Toscano, M. D., Woycechowsky, K. J., and Hilvert, D. (2007) Minimalist active-site redesign: Teaching old enzymes new tricks Angew. Chem., Int. Ed. 46, 4468-4470
-
(2007)
Angew. Chem., Int. Ed.
, vol.46
, pp. 4468-4470
-
-
Toscano, M.D.1
Woycechowsky, K.J.2
Hilvert, D.3
-
2
-
-
77649271939
-
Evolutionary optimization of computationally designed enzymes: Kemp eliminases of the KE07 series
-
Khersonsky, O., Rothlisberger, D., Dym, O., Albeck, S., Jackson, C. J., Baker, D., and Tawfik, D. S. (2010) Evolutionary optimization of computationally designed enzymes: Kemp eliminases of the KE07 series J. Mol. Biol. 396, 1025-1042
-
(2010)
J. Mol. Biol.
, vol.396
, pp. 1025-1042
-
-
Khersonsky, O.1
Rothlisberger, D.2
Dym, O.3
Albeck, S.4
Jackson, C.J.5
Baker, D.6
Tawfik, D.S.7
-
3
-
-
65249154106
-
Toward accurate screening in computer-aided enzyme design
-
Roca, M., Vardi-Kilshtain, A., and Warshel, A. (2009) Toward accurate screening in computer-aided enzyme design Biochemistry 48, 3046-3056
-
(2009)
Biochemistry
, vol.48
, pp. 3046-3056
-
-
Roca, M.1
Vardi-Kilshtain, A.2
Warshel, A.3
-
4
-
-
33748633480
-
Electrostatic basis for enzyme catalysis
-
DOI 10.1021/cr0503106
-
Warshel, A., Sharma, P. K., Kato, M., Xiang, Y., Liu, H., and Olsson, M. H. (2006) Electrostatic basis for enzyme catalysis Chem. Rev. 106, 3210-3235 (Pubitemid 44376933)
-
(2006)
Chemical Reviews
, vol.106
, Issue.8
, pp. 3210-3235
-
-
Warshel, A.1
Sharma, P.K.2
Kato, M.3
Xiang, Y.4
Liu, H.5
Olsson, M.H.M.6
-
6
-
-
0022503114
-
Toward computer-aided site-directed mutagenesis of enzymes
-
Warshel, A. and Sussman, F. (1986) Toward computer-aided site-directed mutagenesis of enzymes Proc. Natl. Acad. Sci. U.S.A. 83, 3806
-
(1986)
Proc. Natl. Acad. Sci. U.S.A.
, vol.83
, pp. 3806
-
-
Warshel, A.1
Sussman, F.2
-
7
-
-
0023659387
-
Semiquantitative calculations of catalytic free energies in genetically modified enzymes
-
Hwang, J. K. and Warshel, A. (1987) Semiquantitative calculations of catalytic free energies in genetically modified enzymes Biochemistry 26, 2669-2673
-
(1987)
Biochemistry
, vol.26
, pp. 2669-2673
-
-
Hwang, J.K.1
Warshel, A.2
-
8
-
-
34249104188
-
The catalytic effect of dihydrofolate reductase and its mutants is determined by reorganization energies
-
DOI 10.1021/bi700201w
-
Liu, H. and Warshel, A. (2007) The Catalytic Effect od Dihydrofolate Reductase and Its Mutants Is Determined by Reorganization Energies Biochemistry 46, 6011-6025 (Pubitemid 46799163)
-
(2007)
Biochemistry
, vol.46
, Issue.20
, pp. 6011-6025
-
-
Liu, H.1
Warshel, A.2
-
9
-
-
23044445638
-
QM/MM modeling the Ras-GAP catalyzed hydrolysis of guanosine triphosphate
-
DOI 10.1002/prot.20472
-
Grigorenko, B. L., Nemukhin, A. V., Topol, I. A., Cachau, R. E., and Burt, S. K. (2005) QM/MM Modeling the Ras-GAP Catalyzed Hydrolysis of Guanosine Triphosphate Proteins 60, 495-503 (Pubitemid 41061641)
-
(2005)
Proteins: Structure, Function and Genetics
, vol.60
, Issue.3
, pp. 495-503
-
-
Grigorenko, B.L.1
Nemukhin, A.V.2
Topol, I.A.3
Cachau, R.E.4
Burt, S.K.5
-
10
-
-
33846110962
-
Computer-aided rational design of catalytic antibodies: The 1F7 case
-
DOI 10.1002/anie.200603293
-
Marti, S., Andres, J., Moliner, V., Silla, E., Tunon, I., and Bertran, J. (2007) Computer-Aided Rational Design of Catalytic Antibodies: The 1F7 Case Angew. Chem., Int. Ed. 46, 286-290 (Pubitemid 46071719)
-
(2007)
Angewandte Chemie - International Edition
, vol.46
, Issue.1-2
, pp. 286-290
-
-
Marti, S.1
Andres, J.2
Silla, E.3
Moliner, V.4
Tunon5
Bertran, J.6
-
11
-
-
41449085516
-
Predicting an improvement of secondary catalytic activity of promiscuos isochorismate pyruvate lyase by computational design
-
DOI 10.1021/ja078334c
-
Marti, S., Andres, J., Moliner, V., Silla, E., Tunon, I., and Bertran, J. (2008) Predicting an Improvement of Secondary Catalytic Activity of Promiscuos Isochorismate Pyruvate Lyase by Computational Design J. Am. Chem. Soc. 130, 2894-2895 (Pubitemid 351455934)
-
(2008)
Journal of the American Chemical Society
, vol.130
, Issue.10
, pp. 2894-2895
-
-
Mati, S.1
Andres, J.2
Moliner, V.3
Silla, E.4
Tunon, I.5
Bertran, J.6
-
12
-
-
39449102395
-
Computational enzymology: Modelling the mechanisms of biological catalysts
-
DOI 10.1042/BST0360022
-
Mulholland, A. J. (2008) Computational enzymology: Modelling the mechanisms of biological catalysts Biochem. Soc. Trans. 36, 22-26 (Pubitemid 351269614)
-
(2008)
Biochemical Society Transactions
, vol.36
, Issue.1
, pp. 22-26
-
-
Mulholland, A.J.1
-
13
-
-
78049316762
-
Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase
-
Frushicheva, M. P., Cao, J., Chu, Z. T., and Warshel, A. (2010) Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase Proc. Natl. Acad. Sci. U.S.A. 107, 16869-16874
-
(2010)
Proc. Natl. Acad. Sci. U.S.A.
, vol.107
, pp. 16869-16874
-
-
Frushicheva, M.P.1
Cao, J.2
Chu, Z.T.3
Warshel, A.4
-
14
-
-
33947086265
-
Physical organic chemistry of benzisoxazoles II. Linearity of the bronsted free energy relationship for the base-catalyzed decomposition of benzisoxazoles
-
Kemp, D. S. and Casey, M. L. (1973) Physical organic chemistry of benzisoxazoles II. Linearity of the bronsted free energy relationship for the base-catalyzed decomposition of benzisoxazoles J. Am. Chem. Soc. 95, 6670-6680
-
(1973)
J. Am. Chem. Soc.
, vol.95
, pp. 6670-6680
-
-
Kemp, D.S.1
Casey, M.L.2
-
15
-
-
17044431448
-
Structural origins of efficient proton abstraction from carbon by a catalytic antibody
-
Debler, E. W., Ito, S., Seebeck, F. P., Heine, A., Hilvert, D., and Wilson, I. A. (2005) Structural origins of efficient proton abstraction from carbon by a catalytic antibody Proc. Natl. Acad. Sci. U.S.A. 102, 4984-4989
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 4984-4989
-
-
Debler, E.W.1
Ito, S.2
Seebeck, F.P.3
Heine, A.4
Hilvert, D.5
Wilson, I.A.6
-
16
-
-
43449098518
-
Kemp elimination catalysts by computational enzyme design
-
DOI 10.1038/nature06879, PII NATURE06879
-
Rothlisberger, D., Khersonsky, O., Wollacott, A. M., Jiang, J., DeChancie, J., Betker, J., Gallaher, J. L., Althoff, E. A., Zanghellini, A., Dym, O., Albeck, S., Houk, K. N., Tawfik, D. S., and Baker, D. (2008) Kemp Elimination Catalysts by Computational Enzyme Design Nature 453, 190-195 (Pubitemid 351667979)
-
(2008)
Nature
, vol.453
, Issue.7192
, pp. 190-195
-
-
Rothlisberger, D.1
Khersonsky, O.2
Wollacott, A.M.3
Jiang, L.4
DeChancie, J.5
Betker, J.6
Gallaher, J.L.7
Althoff, E.A.8
Zanghellini, A.9
Dym, O.10
Albeck, S.11
Houk, K.N.12
Tawfik, D.S.13
Baker, D.14
-
17
-
-
56749170877
-
Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination
-
Alexandrova, A. N., Rothlisberger, D., Baker, D., and Jorgensen, W. L. (2008) Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination J. Am. Chem. Soc. 130, 15907-15915
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 15907-15915
-
-
Alexandrova, A.N.1
Rothlisberger, D.2
Baker, D.3
Jorgensen, W.L.4
-
18
-
-
70449568876
-
Role of water in the multifaceted catalytic antibody 4B2 for allylic isomerization and Kemp elimination reactions
-
Acevedo, O. (2009) Role of water in the multifaceted catalytic antibody 4B2 for allylic isomerization and Kemp elimination reactions J. Phys. Chem. B 113, 15372-15381
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 15372-15381
-
-
Acevedo, O.1
-
19
-
-
77956357583
-
Evaluation and ranking of enzyme designs
-
Kiss, G., Rothlisberger, D., Baker, D., and Houk, K. N. (2010) Evaluation and ranking of enzyme designs Protein Sci. 19, 1760-1773
-
(2010)
Protein Sci.
, vol.19
, pp. 1760-1773
-
-
Kiss, G.1
Rothlisberger, D.2
Baker, D.3
Houk, K.N.4
-
20
-
-
77957750795
-
Conformational diversity and computational enzyme design
-
Lassila, J. K. (2010) Conformational diversity and computational enzyme design Curr. Opin. Chem. Biol. 14, 676-682
-
(2010)
Curr. Opin. Chem. Biol.
, vol.14
, pp. 676-682
-
-
Lassila, J.K.1
-
21
-
-
77951226274
-
At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?
-
Kamerlin, S. C. and Warshel, A. (2010) At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis? Proteins 78, 1339-1375
-
(2010)
Proteins
, vol.78
, pp. 1339-1375
-
-
Kamerlin, S.C.1
Warshel, A.2
-
22
-
-
52449134610
-
Dineopentyl phosphate hydrolysis: Evidence for stepwise water attack
-
Kamerlin, S. C., Williams, N. H., and Warshel, A. (2008) Dineopentyl phosphate hydrolysis: Evidence for stepwise water attack J. Org. Chem. 73, 6960-6969
-
(2008)
J. Org. Chem.
, vol.73
, pp. 6960-6969
-
-
Kamerlin, S.C.1
Williams, N.H.2
Warshel, A.3
-
23
-
-
0028869408
-
Large rate accelerations in antibody catalysis by strategic use of haptenic charge
-
Thorn, S. N., Daniels, R. G., Auditor, M. T., and Hilvert, D. (1995) Large rate accelerations in antibody catalysis by strategic use of haptenic charge Nature 373, 228-230
-
(1995)
Nature
, vol.373
, pp. 228-230
-
-
Thorn, S.N.1
Daniels, R.G.2
Auditor, M.T.3
Hilvert, D.4
-
24
-
-
84961983492
-
Nonspecific medium effects versus specific group positioning in the antibody and albumin catalysis of the base-promoted ring-opening reactions of benzisoxazoles
-
DOI 10.1021/ja0490727
-
Hu, Y., Houk, K. N., Kikuchi, K., Hotta, K., and Hilvert, D. (2004) Nonspecific medium effects versus specific group positioning in the antibody and albumin catalysis of the base-promoted ring-opening reactions of benzisoxazoles J. Am. Chem. Soc. 126, 8197-8205 (Pubitemid 38878965)
-
(2004)
Journal of the American Chemical Society
, vol.126
, Issue.26
, pp. 8197-8205
-
-
Hu, Y.1
Houk, K.N.2
Kikuchi, K.3
Hotta, K.4
Hilvert, D.5
-
25
-
-
73249139757
-
An aspartate and a water molecule mediate efficient acid-base catalysis in a tailored antibody pocket
-
Debler, E. W., Muller, R., Hilvert, D., and Wilson, I. A. (2009) An aspartate and a water molecule mediate efficient acid-base catalysis in a tailored antibody pocket Proc. Natl. Acad. Sci. U.S.A. 106, 18539-18544
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 18539-18544
-
-
Debler, E.W.1
Muller, R.2
Hilvert, D.3
Wilson, I.A.4
-
27
-
-
41849123136
-
A new drug binding subsite on human serum albumin and drug-drug interaction studied by X-ray crystallography
-
Zhu, L., Yang, F., Chen, L., Meehan, E. J., and Huang, M. (2008) A new drug binding subsite on human serum albumin and drug-drug interaction studied by X-ray crystallography J. Struct. Biol. 162, 40-49
-
(2008)
J. Struct. Biol.
, vol.162
, pp. 40-49
-
-
Zhu, L.1
Yang, F.2
Chen, L.3
Meehan, E.J.4
Huang, M.5
-
28
-
-
0034673366
-
Characterization of proton-transfer catalysis by serum albumins
-
DOI 10.1021/ja993471y
-
Hollfelder, F., Kirby, A. J., Tawfik, D. S., Kikuchi, K., and Hilvert, D. (2000) Characterization of Proton-Transfer Catalysis by Serum Albumins J. Am. Chem. Soc. 122, 1022-1029 (Pubitemid 30117435)
-
(2000)
Journal of the American Chemical Society
, vol.122
, Issue.6
, pp. 1022-1029
-
-
Hollfelder, F.1
Kirby, A.J.2
Tawfik, D.S.3
Kikuchi, K.4
Hilvert, D.5
-
29
-
-
71549171901
-
On the energetics of ATP hydrolysis in solution
-
Kamerlin, S. C. and Warshel, A. (2009) On the energetics of ATP hydrolysis in solution J. Phys. Chem. B 113, 15692-15698
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 15692-15698
-
-
Kamerlin, S.C.1
Warshel, A.2
-
30
-
-
74849125160
-
The EVB as a quantitative tool for formulating simulations and analyzing biological and chemical reactions
-
Kamerlin, S. C. and Warshel, A. (2010) The EVB as a quantitative tool for formulating simulations and analyzing biological and chemical reactions Faraday Discuss. 145, 71-106
-
(2010)
Faraday Discuss.
, vol.145
, pp. 71-106
-
-
Kamerlin, S.C.1
Warshel, A.2
-
32
-
-
68149158712
-
On unjustifiably misrepresenting the EVB approach while simultaneously adopting it
-
Kamerlin, S. C., Cao, J., Rosta, E., and Warshel, A. (2009) On unjustifiably misrepresenting the EVB approach while simultaneously adopting it J. Phys. Chem. B 113, 10905-10915
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 10905-10915
-
-
Kamerlin, S.C.1
Cao, J.2
Rosta, E.3
Warshel, A.4
-
33
-
-
0000728542
-
Microscopic and Semimicroscopic Calculations of Electrostatic Energies in Proteins by the Polaris and Enzymix Programs
-
Lee, F. S., Chu, Z. T., and Warshel, A. (1993) Microscopic and Semimicroscopic Calculations of Electrostatic Energies in Proteins by the Polaris and Enzymix Programs J. Comput. Chem. 14, 161-185
-
(1993)
J. Comput. Chem.
, vol.14
, pp. 161-185
-
-
Lee, F.S.1
Chu, Z.T.2
Warshel, A.3
-
34
-
-
77951210462
-
Absolute binding free energy calculations: On the accuracy of computational scoring of protein-ligand interactions
-
Singh, N. and Warshel, A. (2010) Absolute binding free energy calculations: On the accuracy of computational scoring of protein-ligand interactions Proteins 78, 1705-1723
-
(2010)
Proteins
, vol.78
, pp. 1705-1723
-
-
Singh, N.1
Warshel, A.2
-
35
-
-
70349336345
-
Effective approach for calculations of absolute stability of proteins using focused dielectric constants
-
Vicatos, S., Roca, M., and Warshel, A. (2009) Effective approach for calculations of absolute stability of proteins using focused dielectric constants Proteins 77, 670-684
-
(2009)
Proteins
, vol.77
, pp. 670-684
-
-
Vicatos, S.1
Roca, M.2
Warshel, A.3
-
36
-
-
0035943306
-
On the magnitude and specificity of medium effects in enzyme-like catalysts for proton transfer
-
DOI 10.1021/jo015723v
-
Hollfelder, F., Kirby, A. J., and Tawfik, D. S. (2001) On the magnitude and specificity of medium effects in enzyme-like catalysts for proton transfer J. Org. Chem. 66, 5866-5874 (Pubitemid 32867486)
-
(2001)
Journal of Organic Chemistry
, vol.66
, Issue.17
, pp. 5866-5874
-
-
Hollfelder, F.1
Kirby, A.J.2
Tawfik, D.S.3
-
37
-
-
0023645866
-
What about protein polarity?
-
Warshel, A. (1987) What about protein polarity? Nature 330, 15-16
-
(1987)
Nature
, vol.330
, pp. 15-16
-
-
Warshel, A.1
-
39
-
-
77957316716
-
An exciting but challenging road ahead for computational enzyme design
-
Baker, D. (2010) An exciting but challenging road ahead for computational enzyme design Protein Sci. 19, 1817-1819
-
(2010)
Protein Sci.
, vol.19
, pp. 1817-1819
-
-
Baker, D.1
-
40
-
-
4444256797
-
Solvent effects and mechanism for a nucleophilic aromatic substitution from QM/MM simulations
-
DOI 10.1021/ol049121k
-
Acevedo, O. and Jorgensen, W. L. (2004) Solvent effects and mechanism for a nucleophilic aromatic substitution from QM/MM simulations Org. Lett. 6, 2881-2884 (Pubitemid 39178031)
-
(2004)
Organic Letters
, vol.6
, Issue.17
, pp. 2881-2884
-
-
Acevedo, O.1
Jorgensen, W.L.2
-
41
-
-
61949243531
-
Origin of the activity drop with the E50D variant of catalytic antibody 34E4 for Kemp elimination
-
Alexandrova, A. N. and Jorgensen, W. L. (2009) Origin of the activity drop with the E50D variant of catalytic antibody 34E4 for Kemp elimination J. Phys. Chem. B 113, 497-504
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 497-504
-
-
Alexandrova, A.N.1
Jorgensen, W.L.2
-
42
-
-
33644776045
-
Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions
-
DOI 10.1021/jp057109j
-
Rosta, E., Klahn, M., and Warshel, A. (2006) Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions J. Phys. Chem. B 110, 2934-2941 (Pubitemid 43342890)
-
(2006)
Journal of Physical Chemistry B
, vol.110
, Issue.6
, pp. 2934-2941
-
-
Rosta, E.1
Klahn, M.2
Warshel, A.3
-
43
-
-
0034610398
-
Remarkable rate enhancement of orotidine 5′-monophosphate decarboxylase is due to transition-state stabilization rather than to ground-state destabilization
-
Warshel, A., Strajbl, M., Villa, J., and Florian, J. (2000) Remarkable rate enhancement of orotidine 5′-monophosphate decarboxylase is due to transition-state stabilization rather than to ground-state destabilization Biochemistry 39, 14728-14738
-
(2000)
Biochemistry
, vol.39
, pp. 14728-14738
-
-
Warshel, A.1
Strajbl, M.2
Villa, J.3
Florian, J.4
-
44
-
-
68049085675
-
A 21st century revisionists view at a turning point in enzymology
-
Nagel, Z. D. and Klinman, J. P. (2009) A 21st century revisionists view at a turning point in enzymology Nat. Chem. Biol. 5, 543-550
-
(2009)
Nat. Chem. Biol.
, vol.5
, pp. 543-550
-
-
Nagel, Z.D.1
Klinman, J.P.2
|