-
2
-
-
0001858251
-
Application of a Theory of Enzyme Specificity to Protein Synthesis
-
Koshland DE, (1958) Application of a Theory of Enzyme Specificity to Protein Synthesis. Proc Natl Acad Sci USA 44: 98-104.
-
(1958)
Proc Natl Acad Sci USA
, vol.44
, pp. 98-104
-
-
Koshland, D.E.1
-
3
-
-
0024973407
-
Structural plasticity broadens the specificity of an engineered protease
-
Bone R, Silen JL, Agard DA, (1989) Structural plasticity broadens the specificity of an engineered protease. Nature 339: 191-195.
-
(1989)
Nature
, vol.339
, pp. 191-195
-
-
Bone, R.1
Silen, J.L.2
Agard, D.A.3
-
4
-
-
0037013143
-
The conformational plasticity of protein kinases
-
Huse M, Kuriyan J, (2002) The conformational plasticity of protein kinases. Cell 109: 275-282.
-
(2002)
Cell
, vol.109
, pp. 275-282
-
-
Huse, M.1
Kuriyan, J.2
-
5
-
-
33645238421
-
Structural basis for conformational plasticity of the Parkinson's disease-associated ubiquitin hydrolase UCH-L1
-
Das C, Hoang QQ, Kreinbring CA, Luchansky SJ, Meray RK, et al. (2006) Structural basis for conformational plasticity of the Parkinson's disease-associated ubiquitin hydrolase UCH-L1. Proc Natl Acad Sci USA 103: 4675-4680.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 4675-4680
-
-
Das, C.1
Hoang, Q.Q.2
Kreinbring, C.A.3
Luchansky, S.J.4
Meray, R.K.5
-
6
-
-
0041818050
-
Crystal structure of extended-spectrum β-lactamase Toho-1: insights into the molecular mechanism for catalytic reaction and substrate specificity expansion
-
Ibuka AS, Ishii Y, Galleni M, Ishiguro M, Yamaguchi K, et al. (2003) Crystal structure of extended-spectrum β-lactamase Toho-1: insights into the molecular mechanism for catalytic reaction and substrate specificity expansion. Biochemistry 42: 10634-10643.
-
(2003)
Biochemistry
, vol.42
, pp. 10634-10643
-
-
Ibuka, A.S.1
Ishii, Y.2
Galleni, M.3
Ishiguro, M.4
Yamaguchi, K.5
-
7
-
-
33745620493
-
Crystal structure of the Mycobac-terium fortuitum class A β-lactamase: structural basis for broad substrate specificity
-
Sauvage E, Fonze E, Quinting B, Galleni M, Frere JM, et al. (2006) Crystal structure of the Mycobac-terium fortuitum class A β-lactamase: structural basis for broad substrate specificity. Antimicrob Agents Chemother 50: 2516-2521.
-
(2006)
Antimicrob Agents Chemother
, vol.50
, pp. 2516-2521
-
-
Sauvage, E.1
Fonze, E.2
Quinting, B.3
Galleni, M.4
Frere, J.M.5
-
8
-
-
63449139456
-
Structure of P-glycoprotein reveals a molecular basis for poly-specific drug binding
-
Aller SG, Yu J, Ward A, Weng Y, Chittaboina S, et al. (2009) Structure of P-glycoprotein reveals a molecular basis for poly-specific drug binding. Science 323: 1718-1722.
-
(2009)
Science
, vol.323
, pp. 1718-1722
-
-
Aller, S.G.1
Yu, J.2
Ward, A.3
Weng, Y.4
Chittaboina, S.5
-
9
-
-
0028933234
-
Molecular evolution of a class C β-lactamase extending its substrate specificity
-
Nukaga M, Haruta S, Tanimoto K, Kogure K, Taniguchi K, et al. (1995) Molecular evolution of a class C β-lactamase extending its substrate specificity. J Biol Chem 270: 5729-5735.
-
(1995)
J Biol Chem
, vol.270
, pp. 5729-5735
-
-
Nukaga, M.1
Haruta, S.2
Tanimoto, K.3
Kogure, K.4
Taniguchi, K.5
-
10
-
-
0036304570
-
Directed evolution of restriction endonuclease BstYI to achieve increased substrate specificity
-
Samuelson JC, Xu SY, (2002) Directed evolution of restriction endonuclease BstYI to achieve increased substrate specificity. J Mol Biol 319: 673-683.
-
(2002)
J Mol Biol
, vol.319
, pp. 673-683
-
-
Samuelson, J.C.1
Xu, S.Y.2
-
11
-
-
80055109953
-
The molecular basis for the broad substrate specificity of human sulfotransferase 1A1
-
Berger I, Guttman C, Amar D, Zarivach R, Aharoni A, (2011) The molecular basis for the broad substrate specificity of human sulfotransferase 1A1. PLoS ONE 6: e26794.
-
(2011)
PLoS ONE
, vol.6
-
-
Berger, I.1
Guttman, C.2
Amar, D.3
Zarivach, R.4
Aharoni, A.5
-
12
-
-
33845737883
-
Monoterpenes as novel substrates for oxidation and halo-hydroxylation with chloroperoxidase from Caldariomyces fumago
-
Kaup BA, Piantini U, Wust M, Schrader J, (2007) Monoterpenes as novel substrates for oxidation and halo-hydroxylation with chloroperoxidase from Caldariomyces fumago. Appl Microbiol Biotechnol 73: 1087-1096.
-
(2007)
Appl Microbiol Biotechnol
, vol.73
, pp. 1087-1096
-
-
Kaup, B.A.1
Piantini, U.2
Wust, M.3
Schrader, J.4
-
13
-
-
8544219754
-
Site-saturation mutagenesis of Tyr-105 reveals its im-portance in substrate stabilization and discrimination in TEM-1 beta-lactamase
-
Doucet N, De Wals PY, Pelletier JN, (2004) Site-saturation mutagenesis of Tyr-105 reveals its im-portance in substrate stabilization and discrimination in TEM-1 beta-lactamase. J Biol Chem 279: 46295-46303.
-
(2004)
J Biol Chem
, vol.279
, pp. 46295-46303
-
-
Doucet, N.1
de Wals, P.Y.2
Pelletier, J.N.3
-
14
-
-
37849001771
-
A quantitative index of substrate promiscuity
-
Nath A, Atkins WM, (2008) A quantitative index of substrate promiscuity. Biochemistry 47: 157-166.
-
(2008)
Biochemistry
, vol.47
, pp. 157-166
-
-
Nath, A.1
Atkins, W.M.2
-
15
-
-
0017272554
-
Enzyme recruitment in evolution of new function
-
Jensen RA, (1976) Enzyme recruitment in evolution of new function. Annu Rev Microbiol 30: 409-425.
-
(1976)
Annu Rev Microbiol
, vol.30
, pp. 409-425
-
-
Jensen, R.A.1
-
16
-
-
0017771466
-
Evolution and tinkering
-
Jacob F, (1977) Evolution and tinkering. Science 196: 1161-1166.
-
(1977)
Science
, vol.196
, pp. 1161-1166
-
-
Jacob, F.1
-
17
-
-
0037396292
-
Enzymes with extra talents: moonlighting functions and catalytic promiscuity
-
Copley SD, (2003) Enzymes with extra talents: moonlighting functions and catalytic promiscuity. Curr Opin Chem Biol 7: 265-272.
-
(2003)
Curr Opin Chem Biol
, vol.7
, pp. 265-272
-
-
Copley, S.D.1
-
18
-
-
77953623874
-
Enzyme promiscuity: a mechanistic and evolutionary perspective
-
Khersonsky O, Tawfik DS, (2010) Enzyme promiscuity: a mechanistic and evolutionary perspective. Annu Rev Biochem 79: 471-505.
-
(2010)
Annu Rev Biochem
, vol.79
, pp. 471-505
-
-
Khersonsky, O.1
Tawfik, D.S.2
-
19
-
-
82955246714
-
Active site detection by spatial conformity and electrostatic analysis - unravelling a proteolytic function in shrimp alkaline phosphatase
-
Chakraborty S, Minda R, Salaye L, Bhattacharjee SK, Rao BJ, (2011) Active site detection by spatial conformity and electrostatic analysis- unravelling a proteolytic function in shrimp alkaline phosphatase. PLoS ONE 6: e28470.
-
(2011)
PLoS ONE
, vol.6
-
-
Chakraborty, S.1
Minda, R.2
Salaye, L.3
Bhattacharjee, S.K.4
Rao, B.J.5
-
20
-
-
84857124305
-
A measure of the promiscuity of proteins and characteristics of residues in the vicinity of the catalytic site that regulate promiscuity
-
Chakraborty S, Rao BJ, (2012) A measure of the promiscuity of proteins and characteristics of residues in the vicinity of the catalytic site that regulate promiscuity. PLoS ONE 7: e32011.
-
(2012)
PLoS ONE
, vol.7
-
-
Chakraborty, S.1
Rao, B.J.2
-
21
-
-
0029016182
-
Classical electrostatics in biology and chemistry
-
Honig B, Nicholls A, (1995) Classical electrostatics in biology and chemistry. Science 268: 1144-1149.
-
(1995)
Science
, vol.268
, pp. 1144-1149
-
-
Honig, B.1
Nicholls, A.2
-
22
-
-
0035964342
-
Electrostatics of nanosystems: application to microtubules and the ribosome
-
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA, (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci USA 98: 10037-10041.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 10037-10041
-
-
Baker, N.A.1
Sept, D.2
Joseph, S.3
Holst, M.J.4
McCammon, J.A.5
-
23
-
-
62949096122
-
Moonlighting proteins-an update
-
Jeffery CJ, (2009) Moonlighting proteins-an update. Mol Biosyst 5: 345-350.
-
(2009)
Mol Biosyst
, vol.5
, pp. 345-350
-
-
Jeffery, C.J.1
-
24
-
-
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: D129-133.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Porter, C.T.1
Bartlett, G.J.2
Thornton, J.M.3
-
25
-
-
28144441826
-
The bacterial ribosome as a target for antibiotics
-
Poehlsgaard J, Douthwaite S, (2005) The bacterial ribosome as a target for antibiotics. Nat Rev Microbiol 3: 870-881.
-
(2005)
Nat Rev Microbiol
, vol.3
, pp. 870-881
-
-
Poehlsgaard, J.1
Douthwaite, S.2
-
26
-
-
0028963496
-
Erythromycin resistance by ribosome modification
-
Weisblum B, (1995) Erythromycin resistance by ribosome modification. Antimicrob Agents Chemother 39: 577-585.
-
(1995)
Antimicrob Agents Chemother
, vol.39
, pp. 577-585
-
-
Weisblum, B.1
-
27
-
-
0036917889
-
SAM (dependent) I AM: the S-adenosylmethionine-dependent methyltransferase fold
-
Martin JL, McMillan FM, (2002) SAM (dependent) I AM: the S-adenosylmethionine-dependent methyltransferase fold. Curr Opin Struct Biol 12: 783-793.
-
(2002)
Curr Opin Struct Biol
, vol.12
, pp. 783-793
-
-
Martin, J.L.1
McMillan, F.M.2
-
28
-
-
0033522646
-
The 2.2 Å structure of the rRNA methyltransferase ErmC' and its complexes with cofactor and cofactor analogs: implications for the reaction mechanism
-
Schluckebier G, Zhong P, Stewart KD, Kavanaugh TJ, Abad-Zapatero C, (1999) The 2.2 Å structure of the rRNA methyltransferase ErmC' and its complexes with cofactor and cofactor analogs: implications for the reaction mechanism. J Mol Biol 289: 277-291.
-
(1999)
J Mol Biol
, vol.289
, pp. 277-291
-
-
Schluckebier, G.1
Zhong, P.2
Stewart, K.D.3
Kavanaugh, T.J.4
Abad-Zapatero, C.5
-
29
-
-
0032544482
-
ErmE methyltransferase recognition elements in RNA substrates
-
Vester B, Nielsen AK, Hansen LH, Douthwaite S, (1998) ErmE methyltransferase recognition elements in RNA substrates. J Mol Biol 282: 255-264.
-
(1998)
J Mol Biol
, vol.282
, pp. 255-264
-
-
Vester, B.1
Nielsen, A.K.2
Hansen, L.H.3
Douthwaite, S.4
-
30
-
-
50049114778
-
Discovery of protein-palmitoylating enzymes
-
Tsutsumi R, Fukata Y, Fukata M, (2008) Discovery of protein-palmitoylating enzymes. Pflügers Arch 456: 1199-1206.
-
(2008)
Pflügers Arch
, vol.456
, pp. 1199-1206
-
-
Tsutsumi, R.1
Fukata, Y.2
Fukata, M.3
-
31
-
-
82255161850
-
The role of palmitoylation in signalling, cellular trafficking and plasma membrane localization of protease-activated receptor-2
-
Adams MN, Christensen ME, He Y, Waterhouse NJ, Hooper JD, (2011) The role of palmitoylation in signalling, cellular trafficking and plasma membrane localization of protease-activated receptor-2. PLoS ONE 6: e28018.
-
(2011)
PLoS ONE
, vol.6
-
-
Adams, M.N.1
Christensen, M.E.2
He, Y.3
Waterhouse, N.J.4
Hooper, J.D.5
-
32
-
-
0038321812
-
New insights into the mechanisms of protein palmitoylation
-
Linder ME, Deschenes RJ, (2003) New insights into the mechanisms of protein palmitoylation. Bio-chemistry 42: 4311-4320.
-
(2003)
Bio-Chemistry
, vol.42
, pp. 4311-4320
-
-
Linder, M.E.1
Deschenes, R.J.2
-
33
-
-
0034712969
-
The crystal structure of palmitoyl protein thioesterase 1 and the molecular basis of infantile neuronal ceroid lipofuscinosis
-
Bellizzi JJ, Widom J, Kemp C, Lu JY, Das AK, et al. (2000) The crystal structure of palmitoyl protein thioesterase 1 and the molecular basis of infantile neuronal ceroid lipofuscinosis. Proc Natl Acad Sci USA 97: 4573-4578.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 4573-4578
-
-
Bellizzi, J.J.1
Widom, J.2
Kemp, C.3
Lu, J.Y.4
Das, A.K.5
-
34
-
-
0141621057
-
The crystal structure of palmitoyl protein thioesterase-2 (PPT2) reveals the basis for divergent substrate specificities of the two lysosomal thioesterases, PPT1 and PPT2
-
Calero G, Gupta P, Nonato MC, Tandel S, Biehl ER, et al. (2003) The crystal structure of palmitoyl protein thioesterase-2 (PPT2) reveals the basis for divergent substrate specificities of the two lysosomal thioesterases, PPT1 and PPT2. J Biol Chem 278: 37957-37964.
-
(2003)
J Biol Chem
, vol.278
, pp. 37957-37964
-
-
Calero, G.1
Gupta, P.2
Nonato, M.C.3
Tandel, S.4
Biehl, E.R.5
-
35
-
-
0027169561
-
Platelet-activating factor: receptors and signal transduction
-
Chao W, Olson MS, (1993) Platelet-activating factor: receptors and signal transduction. Biochem J 292 (Pt 3): 617-629.
-
(1993)
Biochem J
, vol.292
, Issue.Pt 3
, pp. 617-629
-
-
Chao, W.1
Olson, M.S.2
-
36
-
-
84855183089
-
Platelet-activating factor induces Th17 cell differentiation
-
Drolet AM, Thivierge M, Turcotte S, Hanna D, Maynard B, et al. (2011) Platelet-activating factor induces Th17 cell differentiation. Mediators Inflamm 2011: 913802.
-
(2011)
Mediators Inflamm
, vol.2011
, pp. 913802
-
-
Drolet, A.M.1
Thivierge, M.2
Turcotte, S.3
Hanna, D.4
Maynard, B.5
-
37
-
-
79551554497
-
Platelet activating factor blocks interkinetic nuclear migration in retinal progenitors through an arrest of the cell cycle at the S/G2 transition
-
Fragel-Madeira L, Meletti T, Mariante RM, Monteiro RQ, Einicker-Lamas M, et al. (2011) Platelet activating factor blocks interkinetic nuclear migration in retinal progenitors through an arrest of the cell cycle at the S/G2 transition. PLoS ONE 6: e16058.
-
(2011)
PLoS ONE
, vol.6
-
-
Fragel-Madeira, L.1
Meletti, T.2
Mariante, R.M.3
Monteiro, R.Q.4
Einicker-Lamas, M.5
-
39
-
-
0032859479
-
Probing the substrate specificity of the intracellular brain platelet-activating factor acetylhydrolase
-
Ho YS, Sheffield PJ, Masuyama J, Arai H, Li J, et al. (1999) Probing the substrate specificity of the intracellular brain platelet-activating factor acetylhydrolase. Protein Eng 12: 693-700.
-
(1999)
Protein Eng
, vol.12
, pp. 693-700
-
-
Ho, Y.S.1
Sheffield, P.J.2
Masuyama, J.3
Arai, H.4
Li, J.5
-
40
-
-
0000282461
-
Zinc: biological functions and coordination motifs
-
Vallee BL, Auld DS, (1993) Zinc: biological functions and coordination motifs. Acc. Chem. Res 26: 543-551.
-
(1993)
Acc. Chem. Res
, vol.26
, pp. 543-551
-
-
Vallee, B.L.1
Auld, D.S.2
-
41
-
-
58149251795
-
The 1.4 Å crystal structure of the large and cold-active Vibrio sp. alkaline phosphatase
-
Helland R, Larsen RL, Asgeirsson B, (2009) The 1.4 Å crystal structure of the large and cold-active Vibrio sp. alkaline phosphatase. Biochim Biophys Acta 1794: 297-308.
-
(2009)
Biochim Biophys Acta
, vol.1794
, pp. 297-308
-
-
Helland, R.1
Larsen, R.L.2
Asgeirsson, B.3
-
42
-
-
0037378779
-
Catalysis by ribonuclease A is limited by the rate of substrate association
-
Park C, Raines RT, (2003) Catalysis by ribonuclease A is limited by the rate of substrate association. Biochemistry 42: 3509-3518.
-
(2003)
Biochemistry
, vol.42
, pp. 3509-3518
-
-
Park, C.1
Raines, R.T.2
-
43
-
-
77649239492
-
An efficient, multiply promiscuous hydrolase in the alkaline phosphatase superfamily
-
van Loo B, Jonas S, Babtie AC, Benjdia A, Berteau O, et al. (2010) An efficient, multiply promiscuous hydrolase in the alkaline phosphatase superfamily. Proc Natl Acad Sci USA 107: 2740-2745.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 2740-2745
-
-
van Loo, B.1
Jonas, S.2
Babtie, A.C.3
Benjdia, A.4
Berteau, O.5
-
44
-
-
0001858251
-
Application of a Theory of Enzyme Specificity to Protein Synthesis
-
Koshland DE, (1958) Application of a Theory of Enzyme Specificity to Protein Synthesis. Proc Natl Acad Sci USA 44: 98-104.
-
(1958)
Proc Natl Acad Sci USA
, vol.44
, pp. 98-104
-
-
Koshland, D.E.1
-
45
-
-
3042784274
-
Generating mutant libraries using error-prone PCR
-
Cirino PC, Mayer KM, Umeno D, (2003) Generating mutant libraries using error-prone PCR. Methods Mol Biol 231: 3-9.
-
(2003)
Methods Mol Biol
, vol.231
, pp. 3-9
-
-
Cirino, P.C.1
Mayer, K.M.2
Umeno, D.3
-
46
-
-
0028050350
-
Rapid evolution of a protein in vitro by DNA shuffling
-
Stemmer WP, (1994) Rapid evolution of a protein in vitro by DNA shuffling. Nature 370: 389-391.
-
(1994)
Nature
, vol.370
, pp. 389-391
-
-
Stemmer, W.P.1
-
47
-
-
0031909113
-
Molecular evolution by staggered extension process (StEP) in vitro recombination
-
Zhao H, Giver L, Shao Z, Affholter JA, Arnold FH, (1998) Molecular evolution by staggered extension process (StEP) in vitro recombination. Nat Biotechnol 16: 258-261.
-
(1998)
Nat Biotechnol
, vol.16
, pp. 258-261
-
-
Zhao, H.1
Giver, L.2
Shao, Z.3
Affholter, J.A.4
Arnold, F.H.5
-
48
-
-
0035014185
-
Directed evolution of proteins by exon shuffling
-
Kolkman JA, Stemmer WP, (2001) Directed evolution of proteins by exon shuffling. Nat Biotechnol 19: 423-428.
-
(2001)
Nat Biotechnol
, vol.19
, pp. 423-428
-
-
Kolkman, J.A.1
Stemmer, W.P.2
-
49
-
-
34248567845
-
Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes
-
Reetz MT, Carballeira JD, (2007) Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes. Nat Protoc 2: 891-903.
-
(2007)
Nat Protoc
, vol.2
, pp. 891-903
-
-
Reetz, M.T.1
Carballeira, J.D.2
-
50
-
-
0025146741
-
Saturation site-directed mutagenesis of thymidylate synthase
-
Climie S, Ruiz-Perez L, Gonzalez-Pacanowska D, Prapunwattana P, Cho SW, et al. (1990) Saturation site-directed mutagenesis of thymidylate synthase. J Biol Chem 265: 18776-18779.
-
(1990)
J Biol Chem
, vol.265
, pp. 18776-18779
-
-
Climie, S.1
Ruiz-Perez, L.2
Gonzalez-Pacanowska, D.3
Prapunwattana, P.4
Cho, S.W.5
-
51
-
-
33747234745
-
Expanding the substrate scope of enzymes: combining mutations obtained by CASTing
-
Reetz MT, Carballeira JD, Peyralans J, Hobenreich H, Maichele A, et al. (2006) Expanding the substrate scope of enzymes: combining mutations obtained by CASTing. Chemistry 12: 6031-6038.
-
(2006)
Chemistry
, vol.12
, pp. 6031-6038
-
-
Reetz, M.T.1
Carballeira, J.D.2
Peyralans, J.3
Hobenreich, H.4
Maichele, A.5
-
52
-
-
33751525692
-
New algorithms and an in silico benchmark for computational enzyme design
-
Zanghellini A, Jiang L, Wollacott AM, Cheng G, Meiler J, et al. (2006) New algorithms and an in silico benchmark for computational enzyme design. Protein Sci 15: 2785-2794.
-
(2006)
Protein Sci
, vol.15
, pp. 2785-2794
-
-
Zanghellini, A.1
Jiang, L.2
Wollacott, A.M.3
Cheng, G.4
Meiler, J.5
-
53
-
-
0030793767
-
De novo protein design: fully automated sequence selection
-
Dahiyat BI, Mayo SL, (1997) De novo protein design: fully automated sequence selection. Science 278: 82-87.
-
(1997)
Science
, vol.278
, pp. 82-87
-
-
Dahiyat, B.I.1
Mayo, S.L.2
-
54
-
-
70349330137
-
Automated scaffold selection for enzyme design
-
Malisi C, Kohlbacher O, Hocker B, (2009) Automated scaffold selection for enzyme design. Proteins 77: 74-83.
-
(2009)
Proteins
, vol.77
, pp. 74-83
-
-
Malisi, C.1
Kohlbacher, O.2
Hocker, B.3
-
55
-
-
46449106372
-
The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles
-
Georgiev I, Lilien RH, Donald BR, (2008) The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles. J Comput Chem 29: 1527-1542.
-
(2008)
J Comput Chem
, vol.29
, pp. 1527-1542
-
-
Georgiev, I.1
Lilien, R.H.2
Donald, B.R.3
-
56
-
-
0034663722
-
The penultimate rotamer library
-
Lovell SC, Word JM, Richardson JS, Richardson DC, (2000) The penultimate rotamer library. Proteins 40: 389-408.
-
(2000)
Proteins
, vol.40
, pp. 389-408
-
-
Lovell, S.C.1
Word, J.M.2
Richardson, J.S.3
Richardson, D.C.4
-
57
-
-
84863836923
-
An automated flow for directed evolution based on detection of promiscuous scaffolds using spatial and electrostatic properties of catalytic residues
-
Chakraborty S, (2012) An automated flow for directed evolution based on detection of promiscuous scaffolds using spatial and electrostatic properties of catalytic residues. PLoS ONE 7: e40408.
-
(2012)
PLoS ONE
, vol.7
-
-
Chakraborty, S.1
-
58
-
-
0035807809
-
Enzyme-like proteins by computational design
-
Bolon DN, Mayo SL, (2001) Enzyme-like proteins by computational design. Proc Natl Acad Sci USA 98: 14274-14279.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 14274-14279
-
-
Bolon, D.N.1
Mayo, S.L.2
-
59
-
-
40449116114
-
De novo computational design of retro-aldol enzymes
-
Jiang L, Altho EA, Clemente FR, Doyle L, Rothlisberger D, et al. (2008) De novo computational design of retro-aldol enzymes. Science 319: 1387-1391.
-
(2008)
Science
, vol.319
, pp. 1387-1391
-
-
Jiang, L.1
Altho, E.A.2
Clemente, F.R.3
Doyle, L.4
Rothlisberger, D.5
-
60
-
-
73549117481
-
An artificial di-iron oxo-protein with phenol oxidase activity
-
Faiella M, Andreozzi C, de Rosales RT, Pavone V, Maglio O, et al. (2009) An artificial di-iron oxo-protein with phenol oxidase activity. Nat Chem Biol 5: 882-884.
-
(2009)
Nat Chem Biol
, vol.5
, pp. 882-884
-
-
Faiella, M.1
Andreozzi, C.2
de Rosales, R.T.3
Pavone, V.4
Maglio, O.5
-
61
-
-
77954811495
-
Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction
-
Siegel JB, Zanghellini A, Lovick HM, Kiss G, Lambert AR, et al. (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
-
62
-
-
43449098518
-
Kemp elimination catalysts by computational enzyme design
-
Rothlisberger D, Khersonsky O, Wollacott AM, Jiang L, DeChancie J, et al. (2008) Kemp elimination catalysts by computational enzyme design. Nature 453: 190-195.
-
(2008)
Nature
, vol.453
, pp. 190-195
-
-
Rothlisberger, D.1
Khersonsky, O.2
Wollacott, A.M.3
Jiang, L.4
DeChancie, J.5
-
63
-
-
25844507152
-
Structural and dynamical basis of broad substrate specificity, catalytic mechanism, and inhibition of cytochrome P450 3A4
-
Park H, Lee S, Suh J, (2005) Structural and dynamical basis of broad substrate specificity, catalytic mechanism, and inhibition of cytochrome P450 3A4. J Am Chem Soc 127: 13634-13642.
-
(2005)
J Am Chem Soc
, vol.127
, pp. 13634-13642
-
-
Park, H.1
Lee, S.2
Suh, J.3
-
64
-
-
70350414205
-
Broad substrate specificity and catalytic mechanism of Pseudomonas stutzeri L-rhamnose isomerase: insights from QM/MM molecular dynamics simulations
-
Wu R, Xie H, Mo Y, Cao Z, (2009) Broad substrate specificity and catalytic mechanism of Pseudomonas stutzeri L-rhamnose isomerase: insights from QM/MM molecular dynamics simulations. J Phys Chem A 113: 11595-11603.
-
(2009)
J Phys Chem A
, vol.113
, pp. 11595-11603
-
-
Wu, R.1
Xie, H.2
Mo, Y.3
Cao, Z.4
-
65
-
-
0026049801
-
Serine beta-lactamases and penicillin-binding proteins
-
Ghuysen JM, (1991) Serine beta-lactamases and penicillin-binding proteins. Annu Rev Microbiol 45: 37-67.
-
(1991)
Annu Rev Microbiol
, vol.45
, pp. 37-67
-
-
Ghuysen, J.M.1
-
66
-
-
0033082703
-
The beta-lactamase cycle: a tale of selective pressure and bacterial ingenuity
-
Matagne A, Dubus A, Galleni M, Frere JM, (1999) The beta-lactamase cycle: a tale of selective pressure and bacterial ingenuity. Nat Prod Rep 16: 1-19.
-
(1999)
Nat Prod Rep
, vol.16
, pp. 1-19
-
-
Matagne, A.1
Dubus, A.2
Galleni, M.3
Frere, J.M.4
-
67
-
-
0036829003
-
Structural basis for the beta lactam resistance of PBP2a from methicillin-resistant Staphylococcus aureus
-
Lim D, Strynadka NC, (2002) Structural basis for the beta lactam resistance of PBP2a from methicillin-resistant Staphylococcus aureus. Nat Struct Biol 9: 870-876.
-
(2002)
Nat Struct Biol
, vol.9
, pp. 870-876
-
-
Lim, D.1
Strynadka, N.C.2
-
68
-
-
75149136742
-
Coordination sphere of the third metal site is essential to the activity and metal selectivity of alkaline phosphatases
-
Koutsioulis D, Lyskowski A, Maki S, Guthrie E, Feller G, et al. (2010) Coordination sphere of the third metal site is essential to the activity and metal selectivity of alkaline phosphatases. Protein Sci 75-84.
-
(2010)
Protein Sci
, pp. 75-84
-
-
Koutsioulis, D.1
Lyskowski, A.2
Maki, S.3
Guthrie, E.4
Feller, G.5
-
69
-
-
3242886771
-
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
-
Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA, (2004) PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res 32: W665-667.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Dolinsky, T.J.1
Nielsen, J.E.2
McCammon, J.A.3
Baker, N.A.4
-
70
-
-
18644368714
-
The bioperl toolkit: Perl modules for the life sciences
-
Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, et al. (2002) The bioperl toolkit: Perl modules for the life sciences. Genome Res. 12: 1611-1618.
-
(2002)
Genome Res
, vol.12
, pp. 1611-1618
-
-
Stajich, J.E.1
Block, D.2
Boulez, K.3
Brenner, S.E.4
Chervitz, S.A.5
-
71
-
-
0034201441
-
EMBOSS: the European Molecular Biology Open Software Suite
-
Rice P, Longden I, Bleasby A, (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16: 276-277.
-
(2000)
Trends Genet
, vol.16
, pp. 276-277
-
-
Rice, P.1
Longden, I.2
Bleasby, A.3
-
72
-
-
34548241399
-
Convergent evolution of enzyme active sites is not a rare phenomenon
-
Gherardini PF, Wass MN, Helmer-Citterich M, Sternberg MJ, (2007) Convergent evolution of enzyme active sites is not a rare phenomenon. J Mol Biol 372: 817-845.
-
(2007)
J Mol Biol
, vol.372
, pp. 817-845
-
-
Gherardini, P.F.1
Wass, M.N.2
Helmer-Citterich, M.3
Sternberg, M.J.4
-
73
-
-
0033613813
-
Recognition of spatial motifs in protein structures
-
Kleywegt GJ, (1999) Recognition of spatial motifs in protein structures. J Mol Biol 285: 1887-1897.
-
(1999)
J Mol Biol
, vol.285
, pp. 1887-1897
-
-
Kleywegt, G.J.1
-
74
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul SF, Madden TL, Schaer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaer, A.A.3
Zhang, J.4
Zhang, Z.5
|