-
1
-
-
3543076929
-
Enantioselective biocatalysis optimized by directed evolution
-
Jaeger K.E., and Eggert T. Enantioselective biocatalysis optimized by directed evolution. Curr Opin Biotechnol 15 (2004) 305-313
-
(2004)
Curr Opin Biotechnol
, vol.15
, pp. 305-313
-
-
Jaeger, K.E.1
Eggert, T.2
-
2
-
-
0037408218
-
'Super bugs' for bioremediation
-
Furukawa K. 'Super bugs' for bioremediation. Trends Biotechnol 21 (2003) 187-190
-
(2003)
Trends Biotechnol
, vol.21
, pp. 187-190
-
-
Furukawa, K.1
-
3
-
-
3843148510
-
Development of novel vaccines using DNA shuffling and screening strategies
-
Locher C.P., Soong N.W., Whalen R.G., and Punnonen J. Development of novel vaccines using DNA shuffling and screening strategies. Curr Opin Mol Ther 6 (2004) 34-39
-
(2004)
Curr Opin Mol Ther
, vol.6
, pp. 34-39
-
-
Locher, C.P.1
Soong, N.W.2
Whalen, R.G.3
Punnonen, J.4
-
4
-
-
33745339106
-
Directed evolution by in vitro compartmentalization
-
A comprehensive compilation of protocols were presented for performing directed evolution experiments by in vitro compartmentalization.
-
Miller O.J., Bernath K., Agresti J.J., Amitai G., Kelly B.T., Mastrobattista E., Taly V., Magdassi S., Tawfik D.S., and Griffiths A.D. Directed evolution by in vitro compartmentalization. Nat Methods 3 (2006) 561-570. A comprehensive compilation of protocols were presented for performing directed evolution experiments by in vitro compartmentalization.
-
(2006)
Nat Methods
, vol.3
, pp. 561-570
-
-
Miller, O.J.1
Bernath, K.2
Agresti, J.J.3
Amitai, G.4
Kelly, B.T.5
Mastrobattista, E.6
Taly, V.7
Magdassi, S.8
Tawfik, D.S.9
Griffiths, A.D.10
-
5
-
-
13844250741
-
High-throughput screens and selections of enzyme-encoding genes
-
Aharoni A., Griffiths A.D., and Tawfik D.S. High-throughput screens and selections of enzyme-encoding genes. Curr Opin Chem Biol 9 (2005) 210-216
-
(2005)
Curr Opin Chem Biol
, vol.9
, pp. 210-216
-
-
Aharoni, A.1
Griffiths, A.D.2
Tawfik, D.S.3
-
6
-
-
35148850038
-
Steering directed protein evolution: strategies to manage combinatorial complexity of mutant libraries
-
This review addresses key questions in directed evolution for managing the complexity of mutant libraries from an experimental and a computational point of view.
-
Wong T.S., Roccatano D., and Schwaneberg U. Steering directed protein evolution: strategies to manage combinatorial complexity of mutant libraries. Environ Microbiol 9 (2007) 2645-2659. This review addresses key questions in directed evolution for managing the complexity of mutant libraries from an experimental and a computational point of view.
-
(2007)
Environ Microbiol
, vol.9
, pp. 2645-2659
-
-
Wong, T.S.1
Roccatano, D.2
Schwaneberg, U.3
-
7
-
-
39149125127
-
Enzyme optimization: moving from blind evolution to statistical exploration of sequence-function space
-
Fox R.J., and Huisman G.W. Enzyme optimization: moving from blind evolution to statistical exploration of sequence-function space. Trends Biotechnol 26 (2008) 132-138
-
(2008)
Trends Biotechnol
, vol.26
, pp. 132-138
-
-
Fox, R.J.1
Huisman, G.W.2
-
8
-
-
33846704424
-
Breaking proteins with mutations: threads and thresholds in evolution
-
Bloom J.D., Arnold F.H., and Wilke C.O. Breaking proteins with mutations: threads and thresholds in evolution. Mol Syst Biol 3 (2007) 76
-
(2007)
Mol Syst Biol
, vol.3
, pp. 76
-
-
Bloom, J.D.1
Arnold, F.H.2
Wilke, C.O.3
-
9
-
-
34248674895
-
The stability effects of protein mutations appear to be universally distributed
-
Tokuriki N., Stricher F., Schymkowitz J., Serrano L., and Tawfik D.S. The stability effects of protein mutations appear to be universally distributed. J Mol Biol 369 (2007) 1318-1332
-
(2007)
J Mol Biol
, vol.369
, pp. 1318-1332
-
-
Tokuriki, N.1
Stricher, F.2
Schymkowitz, J.3
Serrano, L.4
Tawfik, D.S.5
-
10
-
-
33845864966
-
Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein
-
Bershtein S., Segal M., Bekerman R., Tokuriki N., and Tawfik D.S. Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein. Nature 444 (2006) 929-932
-
(2006)
Nature
, vol.444
, pp. 929-932
-
-
Bershtein, S.1
Segal, M.2
Bekerman, R.3
Tokuriki, N.4
Tawfik, D.S.5
-
11
-
-
29144503012
-
A statistical analysis of random mutagenesis methods used for directed protein evolution
-
Wong T.S., Roccatano D., Zacharias M., and Schwaneberg U. A statistical analysis of random mutagenesis methods used for directed protein evolution. J Mol Biol 355 (2006) 858-871
-
(2006)
J Mol Biol
, vol.355
, pp. 858-871
-
-
Wong, T.S.1
Roccatano, D.2
Zacharias, M.3
Schwaneberg, U.4
-
12
-
-
48449095514
-
GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries
-
Introduction of new bioinformatics tools to (a) calculates the expected diversity and required library size to sample a mutant library with a predetermined coverage and to (b) choose codons for randomized mutant library construction.
-
Firth A.E., and Patrick W.M. GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries. Nucleic Acids Res 36 (2008) W281-W285. Introduction of new bioinformatics tools to (a) calculates the expected diversity and required library size to sample a mutant library with a predetermined coverage and to (b) choose codons for randomized mutant library construction.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Firth, A.E.1
Patrick, W.M.2
-
13
-
-
54349090614
-
Addressing the numbers problem in directed evolution
-
Reetz M.T., Kahakeaw D., and Lohmer R. Addressing the numbers problem in directed evolution. Chembiochem 9 (2008) 1797-1804
-
(2008)
Chembiochem
, vol.9
, pp. 1797-1804
-
-
Reetz, M.T.1
Kahakeaw, D.2
Lohmer, R.3
-
14
-
-
34248567845
-
Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes
-
The ISM approach offers the possibility of systematic enzyme modifications by saturation mutagenesis of semi-rationally selected positions. With ISM enantioselectivity and thermostability can be enhanced in several iterative rounds by screening of small mutant libraries.
-
Reetz M.T., and Carballeira J.D. Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes. Nat Protoc 2 (2007) 891-903. The ISM approach offers the possibility of systematic enzyme modifications by saturation mutagenesis of semi-rationally selected positions. With ISM enantioselectivity and thermostability can be enhanced in several iterative rounds by screening of small mutant libraries.
-
(2007)
Nat Protoc
, vol.2
, pp. 891-903
-
-
Reetz, M.T.1
Carballeira, J.D.2
-
15
-
-
34548014497
-
Incorporating Synthetic Oligonucleotides via Gene Reassembly (ISOR): a versatile tool for generating targeted libraries
-
Herman A., and Tawfik D.S. Incorporating Synthetic Oligonucleotides via Gene Reassembly (ISOR): a versatile tool for generating targeted libraries. Protein Eng Des Sel 20 (2007) 219-226
-
(2007)
Protein Eng Des Sel
, vol.20
, pp. 219-226
-
-
Herman, A.1
Tawfik, D.S.2
-
16
-
-
49749105153
-
A one-pot, simple methodology for cassette randomisation and recombination for focused directed evolution
-
Hidalgo A., Schliessmann A., Molina R., Hermoso J., and Bornscheuer U.T. A one-pot, simple methodology for cassette randomisation and recombination for focused directed evolution. Protein Eng Des Sel 21 (2008) 567-576
-
(2008)
Protein Eng Des Sel
, vol.21
, pp. 567-576
-
-
Hidalgo, A.1
Schliessmann, A.2
Molina, R.3
Hermoso, J.4
Bornscheuer, U.T.5
-
17
-
-
42649089776
-
Single-step overlap-primer-walk polymerase chain reaction for multiple mutagenesis without overlap extension
-
Kumar R., and Rajagopal K. Single-step overlap-primer-walk polymerase chain reaction for multiple mutagenesis without overlap extension. Anal Biochem 377 (2008) 105-107
-
(2008)
Anal Biochem
, vol.377
, pp. 105-107
-
-
Kumar, R.1
Rajagopal, K.2
-
18
-
-
34948876257
-
Rapid site-directed domain scanning mutagenesis of enteropathogenic Escherichia coli espD
-
Deng Q., Luo W., and Donnenberg M.S. Rapid site-directed domain scanning mutagenesis of enteropathogenic Escherichia coli espD. Biol Proced Online 9 (2007) 18-26
-
(2007)
Biol Proced Online
, vol.9
, pp. 18-26
-
-
Deng, Q.1
Luo, W.2
Donnenberg, M.S.3
-
19
-
-
34248524348
-
Understanding a mechanism of organic cosolvent inactivation in heme monooxygenase P450 BM-3
-
Kuper J., Wong T.S., Roccatano D., Wilmanns M., and Schwaneberg U. Understanding a mechanism of organic cosolvent inactivation in heme monooxygenase P450 BM-3. J Am Chem Soc 129 (2007) 5786-5787
-
(2007)
J Am Chem Soc
, vol.129
, pp. 5786-5787
-
-
Kuper, J.1
Wong, T.S.2
Roccatano, D.3
Wilmanns, M.4
Schwaneberg, U.5
-
20
-
-
36949009858
-
Developments in directed evolution for improving enzyme functions
-
Sen S., Venkata Dasu V., and Mandal B. Developments in directed evolution for improving enzyme functions. Appl Biochem Biotechnol 143 (2007) 212-223
-
(2007)
Appl Biochem Biotechnol
, vol.143
, pp. 212-223
-
-
Sen, S.1
Venkata Dasu, V.2
Mandal, B.3
-
21
-
-
41749117922
-
Trends and challenges in directed evolution
-
Bustos-Jaimes I., and Montiel C. Trends and challenges in directed evolution. Curr Chem Biol 2 (2008) 50-59
-
(2008)
Curr Chem Biol
, vol.2
, pp. 50-59
-
-
Bustos-Jaimes, I.1
Montiel, C.2
-
23
-
-
77952506385
-
Challenges of the genetic code for exploring sequence space in directed protein evolution
-
Wong T.S., Roccatano D., and Schwaneberg U. Challenges of the genetic code for exploring sequence space in directed protein evolution. Biocatal Biotransfor 25 (2007) 229-241
-
(2007)
Biocatal Biotransfor
, vol.25
, pp. 229-241
-
-
Wong, T.S.1
Roccatano, D.2
Schwaneberg, U.3
-
24
-
-
33847016154
-
Are transversion mutations better? A Mutagenesis Assistant Program analysis on P450 BM-3 heme domain
-
Wong T.S., Roccatano D., and Schwaneberg U. Are transversion mutations better? A Mutagenesis Assistant Program analysis on P450 BM-3 heme domain. Biotechnol J 2 (2007) 133-142
-
(2007)
Biotechnol J
, vol.2
, pp. 133-142
-
-
Wong, T.S.1
Roccatano, D.2
Schwaneberg, U.3
-
25
-
-
34147126055
-
Induction of various mutations during PCRs with manganese and 8-hydroxy-dGTP
-
Kamiya H., Ito M., and Harashima H. Induction of various mutations during PCRs with manganese and 8-hydroxy-dGTP. Biol Pharm Bull 30 (2007) 842-844
-
(2007)
Biol Pharm Bull
, vol.30
, pp. 842-844
-
-
Kamiya, H.1
Ito, M.2
Harashima, H.3
-
26
-
-
34247638982
-
RNA mutagenesis yields highly diverse mRNA libraries for in vitro protein evolution
-
Kopsidas G., Carman R.K., Stutt E.L., Raicevic A., Roberts A.S., Siomos M.A., Dobric N., Pontes-Braz L., and Coia G. RNA mutagenesis yields highly diverse mRNA libraries for in vitro protein evolution. BMC Biotechnol 7 (2007) 18
-
(2007)
BMC Biotechnol
, vol.7
, pp. 18
-
-
Kopsidas, G.1
Carman, R.K.2
Stutt, E.L.3
Raicevic, A.4
Roberts, A.S.5
Siomos, M.A.6
Dobric, N.7
Pontes-Braz, L.8
Coia, G.9
-
27
-
-
41149083071
-
A novel random mutagenesis approach using human mutagenic DNA polymerases to generate enzyme variant libraries
-
Emond S., Mondon P., Pizzut-Serin S., Douchy L., Crozet F., Bouayadi K., Kharrat H., Potocki-Veronese G., Monsan P., and Remaud-Simeon M. A novel random mutagenesis approach using human mutagenic DNA polymerases to generate enzyme variant libraries. Protein Eng Des Sel 21 (2008) 267-274
-
(2008)
Protein Eng Des Sel
, vol.21
, pp. 267-274
-
-
Emond, S.1
Mondon, P.2
Pizzut-Serin, S.3
Douchy, L.4
Crozet, F.5
Bouayadi, K.6
Kharrat, H.7
Potocki-Veronese, G.8
Monsan, P.9
Remaud-Simeon, M.10
-
28
-
-
44649102734
-
Improving activity and stability of cutinase towards the anionic detergent AOT by complete saturation mutagenesis
-
Brissos V., Eggert T., Cabral J.M., and Jaeger K.E. Improving activity and stability of cutinase towards the anionic detergent AOT by complete saturation mutagenesis. Protein Eng Des Sel 21 (2008) 387-393
-
(2008)
Protein Eng Des Sel
, vol.21
, pp. 387-393
-
-
Brissos, V.1
Eggert, T.2
Cabral, J.M.3
Jaeger, K.E.4
-
29
-
-
48349098862
-
Expanded molecular diversity generation during directed evolution by trinucleotide exchange (TriNEx)
-
TriNEx is a novel method for generating diversity on the gene level by employing an engineered transposon that randomly substitutes one codon by another.
-
Baldwin A.J., Busse K., Simm A.M., and Jones D.D. Expanded molecular diversity generation during directed evolution by trinucleotide exchange (TriNEx). Nucleic Acids Res 36 (2008) e77. TriNEx is a novel method for generating diversity on the gene level by employing an engineered transposon that randomly substitutes one codon by another.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Baldwin, A.J.1
Busse, K.2
Simm, A.M.3
Jones, D.D.4
-
30
-
-
50549084510
-
Random tag insertions by Transposon Integration mediated Mutagenesis (TIM)
-
Hoeller B.M., Reiter B., Abad S., Graze I., and Glieder A. Random tag insertions by Transposon Integration mediated Mutagenesis (TIM). J Microbiol Methods 75 (2008) 251-257
-
(2008)
J Microbiol Methods
, vol.75
, pp. 251-257
-
-
Hoeller, B.M.1
Reiter, B.2
Abad, S.3
Graze, I.4
Glieder, A.5
-
32
-
-
19644371928
-
One-step random mutagenesis by error-prone rolling circle amplification
-
Fujii R., Kitaoka M., and Hayashi K. One-step random mutagenesis by error-prone rolling circle amplification. Nucleic Acids Res 32 (2004) e145
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Fujii, R.1
Kitaoka, M.2
Hayashi, K.3
-
33
-
-
34547769773
-
Molecular breeding of polymerases for amplification of ancient DNA
-
d'Abbadie M., Hofreiter M., Vaisman A., Loakes D., Gasparutto D., Cadet J., Woodgate R., Paabo S., and Holliger P. Molecular breeding of polymerases for amplification of ancient DNA. Nat Biotechnol 25 (2007) 939-943
-
(2007)
Nat Biotechnol
, vol.25
, pp. 939-943
-
-
d'Abbadie, M.1
Hofreiter, M.2
Vaisman, A.3
Loakes, D.4
Gasparutto, D.5
Cadet, J.6
Woodgate, R.7
Paabo, S.8
Holliger, P.9
-
34
-
-
42149130929
-
Chemical gene synthesis: strategies, softwares, error corrections, and applications
-
Xiong A.S., Peng R.H., Zhuang J., Gao F., Li Y., Cheng Z.M., and Yao Q.H. Chemical gene synthesis: strategies, softwares, error corrections, and applications. FEMS Microbiol Rev 32 (2008) 522-540
-
(2008)
FEMS Microbiol Rev
, vol.32
, pp. 522-540
-
-
Xiong, A.S.1
Peng, R.H.2
Zhuang, J.3
Gao, F.4
Li, Y.5
Cheng, Z.M.6
Yao, Q.H.7
-
35
-
-
0028050350
-
Rapid evolution of a protein in vitro by DNA shuffling
-
Stemmer W.P. Rapid evolution of a protein in vitro by DNA shuffling. Nature 370 (1994) 389-391
-
(1994)
Nature
, vol.370
, pp. 389-391
-
-
Stemmer, W.P.1
-
36
-
-
0031909113
-
Molecular evolution by staggered extension process (StEP) in vitro recombination
-
Zhao H., Giver L., Shao Z., Affholter J.A., and Arnold F.H. Molecular evolution by staggered extension process (StEP) in vitro recombination. Nat Biotechnol 16 (1998) 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
-
37
-
-
33947095042
-
Improving catalytic function by ProSAR-driven enzyme evolution
-
This article describes a statistical analysis of protein sequence-activity relationships for optimization of enzyme properties. ProSAR is based on quantitative structure activity relationship to identify and recombine beneficial mutations in a smart manner.
-
Fox R.J., Davis S.C., Mundorff E.C., Newman L.M., Gavrilovic V., Ma S.K., Chung L.M., Ching C., Tam S., Muley S., et al. Improving catalytic function by ProSAR-driven enzyme evolution. Nat Biotechnol 25 (2007) 338-344. This article describes a statistical analysis of protein sequence-activity relationships for optimization of enzyme properties. ProSAR is based on quantitative structure activity relationship to identify and recombine beneficial mutations in a smart manner.
-
(2007)
Nat Biotechnol
, vol.25
, pp. 338-344
-
-
Fox, R.J.1
Davis, S.C.2
Mundorff, E.C.3
Newman, L.M.4
Gavrilovic, V.5
Ma, S.K.6
Chung, L.M.7
Ching, C.8
Tam, S.9
Muley, S.10
-
38
-
-
34248648171
-
Efficient evolution
-
Evanko D. Efficient evolution. Nat Meth 4 (2007) 300
-
(2007)
Nat Meth
, vol.4
, pp. 300
-
-
Evanko, D.1
-
39
-
-
33947152553
-
Sequence-activity relationships guide directed evolution
-
Pelletier J.N., and Lortie R. Sequence-activity relationships guide directed evolution. Nat Biotechnol 25 (2007) 297-298
-
(2007)
Nat Biotechnol
, vol.25
, pp. 297-298
-
-
Pelletier, J.N.1
Lortie, R.2
-
40
-
-
38949210848
-
Enzyme improvement in the absence of structural knowledge: a novel statistical approach
-
Barak Y., Nov Y., Ackerley D.F., and Matin A. Enzyme improvement in the absence of structural knowledge: a novel statistical approach. ISME J 2 (2008) 171-179
-
(2008)
ISME J
, vol.2
, pp. 171-179
-
-
Barak, Y.1
Nov, Y.2
Ackerley, D.F.3
Matin, A.4
|