Assessing directed evolution methods for the generation of biosynthetic enzymes with potential in drug biosynthesis.

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Published in Future Med Chem on May 01, 2011

Authors

David P Nannemann1, William R Birmingham, Robert A Scism, Brian O Bachmann

Author Affiliations

1: Chemistry Department, 7330 Stevenson Center, Vanderbilt University, Nashville, TN 37235, USA.

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An approach to random mutagenesis of DNA using mixtures of triphosphate derivatives of nucleoside analogues. J Mol Biol (1996) 3.15

Combinatorial cassette mutagenesis as a probe of the informational content of protein sequences. Science (1988) 3.13

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