Methods in Protein Design book cover

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.

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

Included in series
Methods in Enzymology

Hardbound, 520 Pages

Published: March 2013

Imprint: Academic Press

ISBN: 978-0-12-394292-0

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

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