Methods in Protein Design

Content: 
Series Page
Page ii

Copyright
Page iv

Contributors
Pages xi-xvi

Preface
Pages xvii-xviii
Amy E. Keating

Methods in Enzymology
Pages xix-liv

Chapter One - Computational Design of Novel Protein Binders and Experimental Affinity Maturation
Pages 1-19
Timothy A. Whitehead, David Baker, Sarel J. Fleishman

Chapter Two - Mining Tertiary Structural Motifs for Assessment of Designability
Pages 21-40
Jian Zhang, Gevorg Grigoryan

Chapter Three - Computational Methods for Controlling Binding Specificity
Pages 41-59
Oz Sharabi, Ariel Erijman, Julia M. Shifman

Chapter Four - Flexible Backbone Sampling Methods to Model and Design Protein Alternative Conformations
Pages 61-85
Noah Ollikainen, Colin A. Smith, James S. Fraser, Tanja Kortemme

Chapter Five - osprey: Protein Design with Ensembles, Flexibility, and Provable Algorithms
Pages 87-107
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, Bruce R. Donald

Chapter Six - Scientific Benchmarks for Guiding Macromolecular Energy Function Improvement
Pages 109-143
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

Chapter Seven - Molecular Dynamics Simulations for the Ranking, Evaluation, and Refinement of Computationally Designed Proteins
Pages 145-170
Gert Kiss, Vijay S. Pande, K.N. Houk

Chapter Eight - Multistate Protein Design Using CLEVER and CLASSY
Pages 171-190
Christopher Negron, Amy E. Keating

Chapter Nine - Using Analyses of Amino Acid Coevolution to Understand Protein Structure and Function
Pages 191-212
Orr Ashenberg, Michael T. Laub

Chapter Ten - Evolution-Based Design of Proteins
Pages 213-235
Kimberly A. Reynolds, William P. Russ, Michael Socolich, Rama Ranganathan

Chapter Eleven - Protein Engineering and Stabilization from Sequence Statistics: Variation and Covariation Analysis
Pages 237-256
Venuka Durani, Thomas J. Magliery

Chapter Twelve - Enzyme Engineering by Targeted Libraries
Pages 257-283
Moshe Goldsmith, Dan S. Tawfik

Chapter Thirteen - Generation of High-Performance Binding Proteins for Peptide Motifs by Affinity Clamping
Pages 285-302
Shohei Koide, Jin Huang

Chapter Fourteen - Engineering Fibronectin-Based Binding Proteins by Yeast Surface Display
Pages 303-326
Tiffany F. Chen, Seymour de Picciotto, Benjamin J. Hackel, K. Dane Wittrup

Chapter Fifteen - Engineering and Analysis of Peptide-Recognition Domain Specificities by Phage Display and Deep Sequencing
Pages 327-349
Megan E. McLaughlin, Sachdev S. Sidhu

Chapter Sixteen - Efficient Sampling of SCHEMA Chimera Families to Identify Useful Sequence Elements
Pages 351-368
Pete Heinzelman, Philip A. Romero, Frances H. Arnold

Chapter Seventeen - Protein Switch Engineering by Domain Insertion
Pages 369-388
Manu Kanwar, R. Clay Wright, Amol Date, Jennifer Tullman, Marc Ostermeier

Chapter Eighteen - Design of Chimeric Proteins by Combination of Subdomain-Sized Fragments
Pages 389-405
José Arcadio Farías-Rico, Birte Höcker

Chapter Nineteen - О±-Helix Mimicry with О±/ОІ-Peptides
Pages 407-429
Lisa M. Johnson, Samuel H. Gellman

Author Index
Pages 431-452

Subject Index
Pages 453-464