Volume 523: Methods in Protein Design, 1st Edition

Description

This new volume of Methods in Enzymology continues the legacy of this premier serial by containing quality chapters authored by leaders in the field. This volume covers methods in protein design and it has chapters on such topics as protein switch engineering by domain insertion, evolution based design of proteins, and computationally designed proteins.

Methods in Protein Design, 1st Edition

1. Computational Design of Novel Protein Binders and Experimental Affinity Maturation

Timothy A Whitehead, David Baker, and Sarel J Fleishman

2. Mining Tertiary Structural Motifs for Assessment of Designability

Jian Zhang, Gevorg Grigoryan

3. Computational Methods for Controlling Binding Specificity

Oz Sharabi, Ariel Erijman, and Julia M. Shifman

4. Methods in Enzymology: "Flexible Backbone Sampling Methods to Model and Design Protein Alternative Conformations"

Noah Ollikainen, Colin A. Smith, James S. Fraser, Tanja Kortemme

5. OSPREY: Protein Design with Ensembles, Flexibility, and Provable Algorithms

Pablo Gainza, Kyle E. Roberts, Ivelin Georgiev, Ryan H. Lilien, Daniel A. Keedy, Cheng-Yu Chen, Faisal Reza, Amy C. Anderson, David C. Richardson, Jane S. Richardson, and Bruce R. Donald

6. Scientific Benchmarks for Guiding Macromolecular Energy Function Improvement

Andrew Leaver-Fay, Matthew J. O’Meara, Mike Tyka, Ron Jacak, Yifan Song, Elizabeth H. Kellogg, James Thompson, Ian W. Davis, Roland A. Pache, Sergey Lyskov, Jeffrey J. Gray, Tanja Kortemme, Jane S. Richardson, James J. Havranek, Jack Snoeyink, David Baker, Brian Kuhlman

7. Molecular Dynamics Simulations for the Ranking, Evaluation, and Refinement of Computationally Designed Proteins

Gert Kiss, Vijay S. Pande and K. N. Houk

8. Multi-State Protein Design Using CLEVER and CLASSY

Christopher Negron and Amy E. Keating

9. Using Analyses of Amino Acid Coevolution to Understand Protein Structure and Function

Orr Ashenberg and Michael T. Laub

10. Evolution Based Design of Proteins

Kimberly A. Reynolds, William P. Russ, Michael Socolich, and Rama Ranganathan

11. Protein Engineering and Stabilization from Sequence Statistics: Variation and Co-Variation Analysis

Venuka Durani and Thomas J. Magliery

12. Enzyme Engineering by Targeted Libraries

Moshe Goldsmith and Dan S. Tawfik

13. Generation of High-Performance Binding Proteins for Peptide Motifs by Affinity Clamping

Shohei Koide and Jin Huang

14. Engineering Fibronectin-Based Binding Proteins by Yeast Surface Display

Tiffany F. Chen, Seymour de Picciotto, Benjamin J. Hackel, K. Dane Wittrup

15. Engineering and Analysis of Peptide-Recognition Domain Specificities by Phage Display and Deep Sequencing

Megan E. McLaughlin, Sachdev S. Sidhu

16. Efficient Sampling of SCHEMA Chimera Families to Identify Useful Sequence Elements

Pete Heinzelman, Philip A. Romero and Frances H. Arnold

17. Protein Switch Engineering by Domain Insertion

Manu Kanwar, R. Clay Wright, Amol Date, Jennifer Tullman, and Marc Ostermeier

18. Design of Chimeric Proteins by Combination of Subdomain-Sized Fragments

José Arcadio Farias Rico & Birte Höcker

19. a-Helix Mimicry with a/ß-Peptides