Methods in Protein Design

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.
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Biochemists, biophysicists, molecular biologists, analytical chemists, and physiologists


Book information

  • Published: March 2013
  • ISBN: 978-0-12-394292-0

Table of Contents

  1. Computational Design of Novel Protein Binders and Experimental Affinity Maturation
  2. Timothy A Whitehead, David Baker, and Sarel J Fleishman

  3. Mining Tertiary Structural Motifs for Assessment of Designability
  4. Jian Zhang, Gevorg Grigoryan

  5. Computational Methods for Controlling Binding Specificity
  6. Oz Sharabi, Ariel Erijman, and Julia M. Shifman

  7. Methods in Enzymology: "Flexible Backbone Sampling Methods to Model and Design Protein Alternative Conformations"
  8. Noah Ollikainen, Colin A. Smith, James S. Fraser, Tanja Kortemme

  9. OSPREY: Protein Design with Ensembles, Flexibility, and Provable Algorithms
  10. 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

  11. Scientific Benchmarks for Guiding Macromolecular Energy Function Improvement
  12. 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

  13. Molecular Dynamics Simulations for the Ranking, Evaluation, and Refinement of Computationally Designed Proteins
  14. Gert Kiss, Vijay S. Pande and K. N. Houk

  15. Multi-State Protein Design Using CLEVER and CLASSY
  16. Christopher Negron and Amy E. Keating

  17. Using Analyses of Amino Acid Coevolution to Understand Protein Structure and Function
  18. Orr Ashenberg and Michael T. Laub

  19. Evolution Based Design of Proteins
  20. Kimberly A. Reynolds, William P. Russ, Michael Socolich, and Rama Ranganathan

  21. Protein Engineering and Stabilization from Sequence Statistics: Variation and Co-Variation Analysis
  22. Venuka Durani and Thomas J. Magliery

  23. Enzyme Engineering by Targeted Libraries
  24. Moshe Goldsmith and Dan S. Tawfik

  25. Generation of High-Performance Binding Proteins for Peptide Motifs by Affinity Clamping
  26. Shohei Koide and Jin Huang

  27. Engineering Fibronectin-Based Binding Proteins by Yeast Surface Display
  28. Tiffany F. Chen, Seymour de Picciotto, Benjamin J. Hackel, K. Dane Wittrup

  29. Engineering and Analysis of Peptide-Recognition Domain Specificities by Phage Display and Deep Sequencing
  30. Megan E. McLaughlin, Sachdev S. Sidhu

  31. Efficient Sampling of SCHEMA Chimera Families to Identify Useful Sequence Elements
  32. Pete Heinzelman, Philip A. Romero and Frances H. Arnold

  33. Protein Switch Engineering by Domain Insertion
  34. Manu Kanwar, R. Clay Wright, Amol Date, Jennifer Tullman, and Marc Ostermeier

  35. Design of Chimeric Proteins by Combination of Subdomain-Sized Fragments
  36. José Arcadio Farias Rico & Birte Höcker

  37. α-Helix Mimicry with α/β-Peptides

Lisa M. Johnson and Samuel H. Gellman