TY - CHAP AU - Acevedo-Rocha, C. G. AU - Hoebenreich, S. AU - Reetz, M. T. ED - Gillam, E. M. J. ED - Copp, J. N. ED - Ackerley, D. F. PY - 2014 DA - 2014// TI - Iterative saturation mutagenesis: a powerful approach to engineer proteins by systematically simulating Darwinian evolution BT - Directed evolution library creation, methods and protocols PB - Humana Press CY - Totowa ID - Acevedo-Rocha2014 ER - TY - JOUR AU - Akanuma, S. AU - Kigawa, T. AU - Yokoyama, S. PY - 2002 DA - 2002// TI - Combinatorial mutagenesis to restrict amino acid usage in an enzyme to a reduced set JO - Proc Natl Acad Sci USA VL - 99 UR - https://doi.org/10.1073/pnas.222243999 DO - 10.1073/pnas.222243999 ID - Akanuma2002 ER - TY - JOUR AU - Arand, M. AU - Hallberg, B. M. AU - Zou, J. AU - Bergfors, T. AU - Oesch, F. AU - Werf, M. J. AU - Bont, J. A. M. AU - Jones, T. A. AU - Mowbray, S. L. PY - 2003 DA - 2003// TI - Structure of Rhodococcus erythropolis limonene-1,2-epoxide hydrolase reveals a novel active site JO - EMBO J VL - 22 UR - https://doi.org/10.1093/emboj/cdg275 DO - 10.1093/emboj/cdg275 ID - Arand2003 ER - TY - JOUR AU - Bommarius, A. S. PY - 2015 DA - 2015// TI - Biocatalysis: a status report JO - Annu Rev Chem Biomol Eng VL - 6 UR - https://doi.org/10.1146/annurev-chembioeng-061114-123415 DO - 10.1146/annurev-chembioeng-061114-123415 ID - Bommarius2015 ER - TY - JOUR AU - Denard, C. A. AU - Ren, H. AU - Zhao, H. PY - 2015 DA - 2015// TI - Improving and repurposing biocatalysts via directed evolution JO - Curr Opin Chem Biol VL - 25 UR - https://doi.org/10.1016/j.cbpa.2014.12.036 DO - 10.1016/j.cbpa.2014.12.036 ID - Denard2015 ER - TY - JOUR AU - Estell, D. A. AU - Graycar, T. P. AU - Wells, J. A. PY - 1985 DA - 1985// TI - Engineering an enzyme by site-directed mutagenesis to be resistant to chemical oxidation JO - J Biol Chem VL - 260 ID - Estell1985 ER - TY - JOUR AU - Fellouse, F. A. AU - Li, B. AU - Compaan, D. M. AU - Peden, A. A. AU - Hymowitz, S. G. AU - Sidhu, S. S. PY - 2005 DA - 2005// TI - Molecular Recognition by a Binary Code JO - J Mol Biol VL - 348 UR - https://doi.org/10.1016/j.jmb.2005.03.041 DO - 10.1016/j.jmb.2005.03.041 ID - Fellouse2005 ER - TY - STD TI - Glide (2014) Version 6.5. Schrödinger, LLC, New York ID - ref8 ER - TY - JOUR AU - Hopmann, K. H. AU - Hallberg, B. M. AU - Himo, F. PY - 2005 DA - 2005// TI - Catalytic mechanism of limonene epoxide hydrolase, a theoretical study JO - J Am Chem Soc VL - 127 UR - https://doi.org/10.1021/ja050940p DO - 10.1021/ja050940p ID - Hopmann2005 ER - TY - STD TI - Impact (2014) Version 6.5. Schrödinger, LLC, New York ID - ref10 ER - TY - JOUR AU - Kamtekar, S. AU - Schiffer, J. M. AU - Xiong, H. Y. AU - Babik, J. M. AU - Hecht, M. H. PY - 1993 DA - 1993// TI - Protein design by binary patterning of polar and nonpolar amino-acids JO - Science VL - 262 UR - https://doi.org/10.1126/science.8259512 DO - 10.1126/science.8259512 ID - Kamtekar1993 ER - TY - JOUR AU - Koide, A. AU - Gilbreth, R. N. AU - Esaki, K. AU - Tereshko, V. AU - Koide, S. PY - 2007 DA - 2007// TI - High-affinity single-domain binding proteins with a binary-code interface JO - Proc Natl Acad Sci USA VL - 104 UR - https://doi.org/10.1073/pnas.0700149104 DO - 10.1073/pnas.0700149104 ID - Koide2007 ER - TY - JOUR AU - Li, T. AU - Fan, K. AU - Wang, J. AU - Wang, W. PY - 2003 DA - 2003// TI - Reduction of protein sequence complexity by residue grouping JO - Protein Eng Des Sel VL - 16 UR - https://doi.org/10.1093/protein/gzg044 DO - 10.1093/protein/gzg044 ID - Li2003 ER - TY - STD TI - LigPrep (2014) Version 3.2. Schrödinger, LLC, New York ID - ref14 ER - TY - STD TI - Lutz S, Bornscheuer UT (2009) Protein Engineering Handbook. Wiley-VCH, Weinheim ID - ref15 ER - TY - STD TI - Maestro (2014) V10.0. Schrödinger, LLC, New York ID - ref16 ER - TY - JOUR AU - Nov, Y. PY - 2012 DA - 2012// TI - When second best is good enough: another probabilistic look at saturation mutagenesis JO - Appl Environ Microbiol VL - 78 UR - https://doi.org/10.1128/AEM.06265-11 DO - 10.1128/AEM.06265-11 ID - Nov2012 ER - TY - JOUR AU - Olsson, M. H. M. AU - Søndergaard, C. R. AU - Rostkowski, M. AU - Jensen, J. H. PY - 2011 DA - 2011// TI - PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions JO - J Chem Theory Comput VL - 7 UR - https://doi.org/10.1021/ct100578z DO - 10.1021/ct100578z ID - Olsson2011 ER - TY - JOUR AU - Patrick, W. M. AU - Firth, A. E. PY - 2005 DA - 2005// TI - Strategies and computational tools for improving randomized protein libraries JO - Biomol Eng VL - 22 UR - https://doi.org/10.1016/j.bioeng.2005.06.001 DO - 10.1016/j.bioeng.2005.06.001 ID - Patrick2005 ER - TY - STD TI - Prime (2015) Version 3.9. Schrödinger, LLC, New York ID - ref20 ER - TY - JOUR AU - Reetz, M. T. PY - 2011 DA - 2011// TI - Laboratory evolution of stereoselective enzymes: a prolific source of catalysts for asymmetric reactions JO - Angew Chem Int Ed VL - 50 UR - https://doi.org/10.1002/anie.201000826 DO - 10.1002/anie.201000826 ID - Reetz2011 ER - TY - JOUR AU - Reetz, M. T. AU - Carballeira, J. D. PY - 2007 DA - 2007// TI - Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes JO - Nat Protocols VL - 2 UR - https://doi.org/10.1038/nprot.2007.72 DO - 10.1038/nprot.2007.72 ID - Reetz2007 ER - TY - JOUR AU - Reetz, M. T. AU - Wilensek, S. AU - Zha, D. AU - Jaeger, K. E. PY - 2001 DA - 2001// TI - Directed evolution of an enantioselective enzyme through combinatorial multiple-cassette mutagenesis JO - Angew Chem Int Ed VL - 40 UR - https://doi.org/3.0.CO;2-X DO - 3.0.CO;2-X ID - Reetz2001 ER - TY - JOUR AU - Reetz, M. T. AU - Bocola, M. AU - Carballeira, J. D. AU - Zha, D. AU - Vogel, A. PY - 2005 DA - 2005// TI - Expanding the range of substrate acceptance of enzymes: combinatorial active-site saturation test JO - Angew Chem Int Ed VL - 44 UR - https://doi.org/10.1002/anie.200500767 DO - 10.1002/anie.200500767 ID - Reetz2005 ER - TY - JOUR AU - Reetz, M. T. AU - Wang, L. W. AU - Bocola, M. PY - 2006 DA - 2006// TI - Directed evolution of enantioselective enzymes: iterative cycles of CASTing for probing protein-sequence space JO - Angew Chem Int Ed VL - 45 UR - https://doi.org/10.1002/anie.200502746 DO - 10.1002/anie.200502746 ID - Reetz2006 ER - TY - JOUR AU - Roy, S. AU - Hecht, M. H. PY - 2000 DA - 2000// TI - Cooperative thermal denaturation of proteins designed by binary patterning of polar and nonpolar amino acids JO - Biochemistry VL - 39 UR - https://doi.org/10.1021/bi992328e DO - 10.1021/bi992328e ID - Roy2000 ER - TY - STD TI - Schrödinger Suite 2015-1 (2015) Protein Preparation Wizard; Epik version 3.1, Schrödinger, LLC, New York, NY, 2015; Impact version 6.6, Schrödinger, LLC, New York, NY, 2015; Prime version 3.9, Schrödinger, LLC, New York ID - ref27 ER - TY - JOUR AU - Sun, Z. AU - Lonsdale, R. AU - Kong, X. D. AU - Xu, J. H. AU - Zhou, J. AU - Reetz, M. T. PY - 2015 DA - 2015// TI - Reshaping an enzyme binding pocket for enhanced and inverted stereoselectivity: use of smallest amino acid alphabets in directed evolution JO - Angew Chem Int Ed VL - 54 UR - https://doi.org/10.1002/anie.201501809 DO - 10.1002/anie.201501809 ID - Sun2015 ER - TY - JOUR AU - Sun, Z. AU - Wikmark, Y. AU - Bäckvall, J. -. E. AU - Reetz, M. T. PY - 2016 DA - 2016// TI - New concepts for increasing the efficiency in directed evolution of stereoselective enzymes JO - Chem Eur J VL - 22 UR - https://doi.org/10.1002/chem.201504406 DO - 10.1002/chem.201504406 ID - Sun2016 ER - TY - JOUR AU - Sun, Z. AU - Lonsdale, R. AU - Wu, L. AU - Li, G. AU - Li, A. AU - Wang, J. AU - Zhou, J. AU - Reetz, M. T. PY - 2016 DA - 2016// TI - Structure-guided triple-code saturation mutagenesis: efficient tuning of the stereoselectivity of an epoxide hydrolase JO - ACS Catalysis VL - 6 UR - https://doi.org/10.1021/acscatal.5b02751 DO - 10.1021/acscatal.5b02751 ID - Sun2016 ER - TY - JOUR AU - Sun, Z. AU - Lonsdale, R. AU - Li, G. AU - Reetz, M. T. PY - 2016 DA - 2016// TI - Comparing different strategies in directed evolution of enzyme stereoselectivity: single- versus double-code saturation mutagenesis JO - ChemBioChem. ID - Sun2016 ER - TY - JOUR AU - Werf, M. J. AU - Overkamp, K. M. AU - Bont, J. A. M. PY - 1998 DA - 1998// TI - Limonene-1,2-epoxide hydrolase from rhodococcus erythropolis DCL14 belongs to a novel class of epoxide hydrolases JO - J Bacteriol VL - 180 ID - Werf1998 ER - TY - JOUR AU - Wahler, D. AU - Reymond, J. L. PY - 2002 DA - 2002// TI - The adrenaline test for enzymes JO - Angew Chem Int Ed VL - 41 UR - https://doi.org/3.0.CO;2-5 DO - 3.0.CO;2-5 ID - Wahler2002 ER - TY - JOUR AU - Walter, K. U. AU - Vamvaca, K. AU - Hilvert, D. PY - 2005 DA - 2005// TI - An active enzyme constructed from a 9-amino acid alphabet JO - J Biol Chem VL - 280 UR - https://doi.org/10.1074/jbc.M507210200 DO - 10.1074/jbc.M507210200 ID - Walter2005 ER - TY - CHAP AU - Williams, E. AU - Copp, J. N. AU - Ackerley, D. F. ED - Gillam, E. M. J. ED - Copp, J. N. ED - Ackerley, D. F. PY - 2014 DA - 2014// TI - Site-saturation mutagenesis by overlap extension PCR BT - Directed evolution library creation, methods and protocols PB - Humana Press CY - Totowa ID - Williams2014 ER - TY - JOUR AU - Zheng, H. AU - Reetz, M. T. PY - 2010 DA - 2010// TI - Manipulating the stereoselectivity of limonene epoxide hydrolase by directed evolution based on iterative saturation mutagenesis JO - J Am Chem Soc VL - 132 UR - https://doi.org/10.1021/ja1067542 DO - 10.1021/ja1067542 ID - Zheng2010 ER -