-
2
-
-
17744387944
-
De novo design of a redox-active minimal rubredoxin mimic
-
DOI 10.1021/ja050553f
-
Nanda V, Rosenblatt MM, Osyczka A, Kono H, Getahun Z, Dutton PL, Saven JG, Degrado WF (2005) De novo design of a redox-active minimal rubredoxin mimic. J Am Chem Soc 127:5804-5805. (Pubitemid 40577635)
-
(2005)
Journal of the American Chemical Society
, vol.127
, Issue.16
, pp. 5804-5805
-
-
Nanda, V.1
Rosenblatt, M.M.2
Osyczka, A.3
Kono, H.4
Getahun, Z.5
Dutton, P.L.6
Saven, J.G.7
DeGrado, W.F.8
-
3
-
-
43449098518
-
Kemp elimination catalysts by computational enzyme design
-
DOI 10.1038/nature06879, PII NATURE06879
-
Rothlisberger D, Khersonsky O, Wollacott AM, Jiang L, DeChancie J, Betker J, Gallaher JL, Althoff EA, Zanghellini A, Dym O, Albeck S, Houk KN, Tawfik DS, 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
-
4
-
-
40449116114
-
De novo computational design of retro-aldol enzymes
-
DOI 10.1126/science.1152692
-
Jiang L, Althoff EA, Clemente FR, Doyle L, Rothlisberger D, Zanghellini A, Gallaher JL, Betker JL, Tanaka F, Barbas CF III, Hilvert D, Houk KN, Stoddard BL, Baker D (2008) De novo computational design of retro-aldol enzymes. Science 319:1387-1391. (Pubitemid 351354873)
-
(2008)
Science
, vol.319
, Issue.5868
, pp. 1387-1391
-
-
Jiang, L.1
Althoff, E.A.2
Clemente, F.R.3
Doyle, L.4
Rothlisberger, D.5
Zanghellini, A.6
Gallaher, J.L.7
Betker, J.L.8
Tanaka, F.9
Barbas III, C.F.10
Hilvert, D.11
Houk, K.N.12
Stoddard, B.L.13
Baker, D.14
-
5
-
-
72949111166
-
Rational design of a structural and functional nitric oxide reductase
-
Yeung N, Lin YW, Gao YG, Zhao X, Russell BS, Lei L, Miner KD, Robinson H, Lu Y (2009) Rational design of a structural and functional nitric oxide reductase. Nature 462:1079-1082.
-
(2009)
Nature
, vol.462
, pp. 1079-1082
-
-
Yeung, N.1
Lin, Y.W.2
Gao, Y.G.3
Zhao, X.4
Russell, B.S.5
Lei, L.6
Miner, K.D.7
Robinson, H.8
Lu, Y.9
-
6
-
-
77954811495
-
Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction
-
Siegel JB, Zanghellini A, Lovick HM, Kiss G, Lambert AR, St Clair JL, Gallaher JL, Hilvert D, Gelb MH, Stoddard BL, Houk KN, Michael FE, Baker D (2010) Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science 329:309-313.
-
(2010)
Science
, vol.329
, pp. 309-313
-
-
Siegel, J.B.1
Zanghellini, A.2
Lovick, H.M.3
Kiss, G.4
Lambert, A.R.5
St Clair, J.L.6
Gallaher, J.L.7
Hilvert, D.8
Gelb, M.H.9
Stoddard, B.L.10
Houk, K.N.11
Michael, F.E.12
Baker, D.13
-
7
-
-
0032253961
-
Theozymes and compuzymes: Theoretical models for biological catalysis
-
Tantillo DJ, Chen J, Houk KN (1998) Theozymes and compuzymes: theoretical models for biological catalysis. Curr Opin Chem Biol 2:743-750. (Pubitemid 128646745)
-
(1998)
Current Opinion in Chemical Biology
, vol.2
, Issue.6
, pp. 743-750
-
-
Tantillo, D.J.1
Chen, J.2
Houk, K.N.3
-
9
-
-
33751525692
-
New algorithms and an in silico benchmark for computational enzyme design
-
DOI 10.1110/ps.062353106
-
Zanghellini A, Jiang L, Wollacott AM, Cheng G, Meiler J, Althoff EA, Rothlisberger D, Baker D (2006) New algorithms and an in silico benchmark for computational enzyme design. Protein Sci 15:2785-2794. (Pubitemid 44833759)
-
(2006)
Protein Science
, vol.15
, Issue.12
, pp. 2785-2794
-
-
Zanghellini, A.1
Jiang, L.2
Wollacott, A.M.3
Cheng, G.4
Meiler, J.5
Althoff, E.A.6
Rothlisberger, D.7
Baker, D.8
-
11
-
-
0000230329
-
Energetics of enzyme catalysis
-
Warshel A (1978) Energetics of enzyme catalysis. Proc Natl Acad Sci USA 75:5250-5254.
-
(1978)
Proc Natl Acad Sci USA
, vol.75
, pp. 5250-5254
-
-
Warshel, A.1
-
12
-
-
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
-
13
-
-
33748633480
-
Electrostatic basis for enzyme catalysis
-
DOI 10.1021/cr0503106
-
Warshel A, Sharma PK, Kato M, Xiang Y, Liu H, Olsson MH (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
-
14
-
-
13644271603
-
Positional ordering of reacting groups contributes significantly to the efficiency of proton transfer at an antibody active site
-
DOI 10.1021/ja044647l
-
Seebeck FP, Hilvert D (2005) Positional ordering of reacting groups contributes significantly to the efficiency of proton transfer at an antibody active site. J Am Chem Soc 127:1307-1312. (Pubitemid 40228701)
-
(2005)
Journal of the American Chemical Society
, vol.127
, Issue.4
, pp. 1307-1312
-
-
Seebeck, F.P.1
Hilvert, D.2
-
15
-
-
56449128760
-
Structural reorganization and preorganization in enzyme active sites: Comparisons of experimental and theoretically ideal active site geometries in the multistep serine esterase reaction cycle
-
Smith AJ, Muller R, Toscano MD, Kast P, Hellinga HW, Hilvert D, Houk KN (2008) Structural reorganization and preorganization in enzyme active sites: comparisons of experimental and theoretically ideal active site geometries in the multistep serine esterase reaction cycle. J Am Chem Soc 130:15361-15373.
-
(2008)
J Am Chem Soc
, vol.130
, pp. 15361-15373
-
-
Smith, A.J.1
Muller, R.2
Toscano, M.D.3
Kast, P.4
Hellinga, H.W.5
Hilvert, D.6
Houk, K.N.7
-
16
-
-
34548445989
-
How similar are enzyme active site geometries derived from quantum mechanical theozymes to crystal structures of enzyme-inhibitor complexes? Implications for enzyme design
-
DOI 10.1110/ps.072963707
-
Dechancie J, Clemente FR, Smith AJ, Gunaydin H, Zhao YL, Zhang X, Houk KN (2007) How similar are enzyme active site geometries derived from quantum mechanical theozymes to crystal structures of enzyme-inhibitor complexes? Implications for enzyme design. Protein Sci 16:1851-1866. (Pubitemid 47367108)
-
(2007)
Protein Science
, vol.16
, Issue.9
, pp. 1851-1866
-
-
DeChancie, J.1
Clemente, F.R.2
Smith, A.J.T.3
Gunaydin, H.4
Zhao, Y.-L.5
Zhang, X.6
Houk, K.N.7
-
17
-
-
34250156703
-
Exhaustive mutagenesis of six secondary active-site residues in Escherichia coli chorismate mutase shows the importance of hydrophobic side chains and a helix N-capping position for stability and catalysis
-
DOI 10.1021/bi700215x
-
Lassila JK, Keeffe JR, Kast P, Mayo SL (2007) Exhaustive mutagenesis of six secondary active-site residues in Escherichia coli chorismate mutase shows the importance of hydrophobic side chains and a helix N-capping position for stability and catalysis. Biochemistry 46:6883-6891. (Pubitemid 46906417)
-
(2007)
Biochemistry
, vol.46
, Issue.23
, pp. 6883-6891
-
-
Lassila, J.K.1
Keeffe, J.R.2
Kast, P.3
Mayo, S.L.4
-
18
-
-
70349632843
-
The influence of protein dynamics on the success of computational enzyme design
-
Ruscio JZ, Kohn JE, Ball KA, Head-Gordon T (2009) The influence of protein dynamics on the success of computational enzyme design. J Am Chem Soc 131:14111-14115.
-
(2009)
J Am Chem Soc
, vol.131
, pp. 14111-14115
-
-
Ruscio, J.Z.1
Kohn, J.E.2
Ball, K.A.3
Head-Gordon, T.4
-
19
-
-
33646935697
-
Dynamical contributions to enzyme catalysis: Critical tests of a popular hypothesis
-
DOI 10.1021/cr040427e
-
Olsson MH, Parson WW, Warshel A (2006) Dynamical contributions to enzyme catalysis: critical tests of a popular hypothesis. Chem Rev 106:1737-1756. (Pubitemid 43792778)
-
(2006)
Chemical Reviews
, vol.106
, Issue.5
, pp. 1737-1756
-
-
Olsson, M.H.M.1
Parson, W.W.2
Warshel, A.3
-
21
-
-
77951226274
-
At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?
-
Kamerlin SC, 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
-
24
-
-
65249143885
-
Enzyme (re)design: Lessons from natural evolution and computation
-
Gerlt JA, Babbitt PC (2009) Enzyme (re)design: Lessons from natural evolution and computation. Curr Opin Chem Biol 13:10-18.
-
(2009)
Curr Opin Chem Biol
, vol.13
, pp. 10-18
-
-
Gerlt, J.A.1
Babbitt, P.C.2
-
25
-
-
42149085208
-
An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design
-
DOI 10.1002/jcc.20878
-
Vizcarra CL, Zhang N, Marshall SA, Wingreen NS, Zeng C, Mayo SL (2008) An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design. J Comput Chem 29:1153-1162. (Pubitemid 351535412)
-
(2008)
Journal of Computational Chemistry
, vol.29
, Issue.7
, pp. 1153-1162
-
-
Vizcarra, C.L.1
Zhang, N.2
Marshall, S.A.3
Wingreen, N.S.4
Zeng, C.5
Mayo, S.L.6
-
26
-
-
79953310914
-
Optimizing non-natural protein function with directed evolution
-
Brustad EM, Arnold FH (2011) Optimizing non-natural protein function with directed evolution. Curr Opin Chem Biol 15:201-210.
-
(2011)
Curr Opin Chem Biol
, vol.15
, pp. 201-210
-
-
Brustad, E.M.1
Arnold, F.H.2
-
27
-
-
0026335211
-
Construction of new ligand binding sites in proteins of known structure. I. Computer-aided modeling of sites with pre-defined geometry
-
Hellinga HW, Richards FM (1991) Construction of new ligand binding sites in proteins of known structure. I. Computer-aided modeling of sites with pre-defined geometry. J Mol Biol 222:763-785.
-
(1991)
J Mol Biol
, vol.222
, pp. 763-785
-
-
Hellinga, H.W.1
Richards, F.M.2
-
28
-
-
0037780207
-
8-barrels: Functional promiscuity produced by single substitutions in the enolase superfamily
-
DOI 10.1021/bi034769a
-
Schmidt DM, Mundorff EC, Dojka M, Bermudez E, Ness JE, Govindarajan S, Babbitt PC, Minshull J, Gerlt JA (2003) Evolutionary potential of (beta/alpha)8- barrels: Functional promiscuity produced by single substitutions in the enolase superfamily. Biochemistry 42:8387-8393. (Pubitemid 36875403)
-
(2003)
Biochemistry
, vol.42
, Issue.28
, pp. 8387-8393
-
-
Schmidt, D.M.Z.1
Mundorff, E.C.2
Dojka, M.3
Bermudez, E.4
Ness, J.E.5
Govindarajan, S.6
Babbitt, P.C.7
Minshull, J.8
Gerlt, J.A.9
-
29
-
-
24344494387
-
8-barrels: In vitro enhancement of a "new" reaction in the enolase superfamily
-
DOI 10.1021/bi050963g
-
Vick JE, Schmidt DM, Gerlt JA (2005) Evolutionary potential of (beta/alpha)8-barrels: in vitro enhancement of a "new" reaction in the enolase superfamily. Biochemistry 44:11722-11729. (Pubitemid 41262706)
-
(2005)
Biochemistry
, vol.44
, Issue.35
, pp. 11722-11729
-
-
Vick, J.E.1
Schmidt, D.M.Z.2
Gerlt, J.A.3
-
30
-
-
37249087129
-
8-barrels: Stepwise evolution of a "new" reaction in the enolase superfamily
-
DOI 10.1021/bi7019063
-
Vick JE, Gerlt JA (2007) Evolutionary potential of (beta/alpha)8-barrels: stepwise evolution of a "new" reaction in the enolase superfamily. Biochemistry 46:14589-14597. (Pubitemid 350276364)
-
(2007)
Biochemistry
, vol.46
, Issue.50
, pp. 14589-14597
-
-
Vick, J.E.1
Gerlt, J.A.2
-
31
-
-
0029988963
-
Transition state of the base-promoted ring-opening of isoxazoles. Theoretical prediction of catalytic functionalities and design of haptens for antibody production
-
DOI 10.1021/ja953550j
-
Na J, Houk KN, Hilvert D (1996) Transition state of the base-promoted ring-opening of isoxazoles. Theoretical prediction of catalytic functionalities and design of haptens for antibody production. J Am Chem Soc 118:6462-6471. (Pubitemid 26247700)
-
(1996)
Journal of the American Chemical Society
, vol.118
, Issue.27
, pp. 6462-6471
-
-
Na, J.1
Houk, K.N.2
Hilvert, D.3
-
32
-
-
0141850386
-
An algorithm for constraint-based structural template matching: Application to 3D templates with statistical analysis
-
DOI 10.1093/bioinformatics/btg226
-
Barker JA, Thornton JM (2003) An algorithm for con-straint- based structural template matching: application to 3D templates with statistical analysis. Bioinformatics 19:1644-1649. (Pubitemid 37121152)
-
(2003)
Bioinformatics
, vol.19
, Issue.13
, pp. 1644-1649
-
-
Barker, J.A.1
Thornton, J.M.2
-
33
-
-
0345864027
-
The Catalytic Site Atlas: A resource of catalytic sites and residues identified in enzymes using structural data
-
Porter CT, Bartlett GJ, Thornton JM (2004) The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res 32:D129-D133. (Pubitemid 38081621)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.DATABASE ISS.
-
-
Porter, C.T.1
Bartlett, G.J.2
Thornton, J.M.3
-
35
-
-
79951476387
-
PROPKA3: Consistent treatment of internal and surface residues in empirical pK(a) predictions
-
Olsson MHM, Sondergaard CR, Rostkowski M, Jensen JH (2011) PROPKA3: consistent treatment of internal and surface residues in empirical pK(a) predictions. J Chem Theory Comput 7:525-537.
-
(2011)
J Chem Theory Comput
, vol.7
, pp. 525-537
-
-
Olsson, M.H.M.1
Sondergaard, C.R.2
Rostkowski, M.3
Jensen, J.H.4
|