Enzyme Engineering and Evolution: General Methods. Methods in Enzymology Volume 643

Table of Contents

1. In vivo site-directed recombination (SDR): An efficient tool to reveal beneficial epistasis

Javier Vi?a-Gonzalez and Miguel Alcalde

2. A beginner's guide to molecular dynamics simulations and the identification of cross-correlation networks for enzyme engineering

Haoran Yu and Paul A. Dalby

3. Exploration of enzyme diversity: High-throughput techniques for protein production and microscale biochemical characterization

Michal Vasina, Pavel Vanacek, Jiri Damborsky and Zbynek Prokop

4. Emulsion-based directed evolution of enzymes and proteins in yeast

Elizabeth C. Gardner, Ella J. Watkins, Jimmy Gollihar and Andrew D. Ellington

5. Remodeling enzyme active sites by stepwise loop insertion

Md Anarul Hoque, Yong Zhang, Li Zhi, Li Cui and Yan Feng

6. Consensus Finder web tool to predict stabilizing substitutions in proteins

Bryan J. Jones, Chi Nok Enoch Kan, Christine Luo and Romas J. Kazlauskas

7. The use of consensus sequence information to engineer stability and activity in proteins

Matt Sternke, Katherine W. Tripp and Doug Barrick

8. Structure-guided rational design of the substrate specificity and catalytic activity of an enzyme

Jung Min Choi and Hak-Sung Kim

9. Biological fitness landscapes by deep mutational scanning

Jacob D. Mehlhoff and Marc Ostermeier

10. Focused rational iterative site-specific mutagenesis (FRISM)

Danyang Li, Qi Wu and Manfred T. Reetz

11. Statistical analysis of mutational epistasis to reveal intramolecular interaction networks in proteins

Charlotte M. Miton, John Z. Chen, Kalum Ost, Dave W. Anderson and Nobuhiko Tokuriki

12. Machine learning-assisted enzyme engineering

Niklas E. Siedhoff, Ulrich Schwaneberg and Mehdi D. Davari

13. Ultrahigh throughput screening for enzyme function in droplets

Stefanie Neun, Paul J. Zurek, Tomasz S. Kaminski and Florian Hollfelder