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.

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


    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. ?-Helix Mimicry with ?/?-Peptides
      Lisa M. Johnson and Samuel H. Gellman


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