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.

Key Features

  • Continues the legacy of this premier serial with quality chapters authored by leaders in the field
  • Covers methods in protein design
  • Contains chapters with such topics as protein switch engineering by domain insertion, evolution-based design of proteins, and computationally designed proteins

Readership

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

Table of Contents

Contributors

Preface

Methods in Enzymology

Chapter One. Computational Design of Novel Protein Binders and Experimental Affinity Maturation

Abstract

1 Introduction

2 Computational Design of Binders Using Novel Scaffolds

3 Target Selection

4 Generating an Idealized Concept of the Hotspot

5 Selecting Shape Complementary Scaffold Surfaces for Design

6 Interface Design

7 Yeast Cell-Surface Display as a Screening Method for Designed Binders

8 Affinity Maturation

9 What Works, What Fails, and What It Means

Acknowledgments

References

Chapter Two. Mining Tertiary Structural Motifs for Assessment of Designability

Abstract

1 Introduction

2 MaDCaT

3 Quantifying Designability

4 Further Developments

5 Summary

Acknowledgments

References

Chapter Three. Computational Methods for Controlling Binding Specificity

Abstract

1 Introduction

2 Narrowing Down Binding Specificity

3 Broadening Binding Specificity

4 Summary

Acknowledgments

References

Chapter Four. Flexible Backbone Sampling Methods to Model and Design Protein Alternative Conformations

Abstract

1 Introduction

2 Rosetta Moves to Model Alternative Conformations in X-Ray Density

3 Sequence Plasticity and Conformational Plasticity are Intertwined

4 Future Challenges

Acknowledgments

References

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

Abstract

1 Introduction

2 OSPREY Design Principles

3 Applications of OSPREY

4 Protein Design in OSPREY

5 Example: Predicting Drug Resistance Mutations Using OSPREY

6 Future Directions and Availability

Acknowledgments

References

Chapter Six. Scientific B

Details

No. of pages:
520
Language:
English
Copyright:
© 2013
Published:
Imprint:
Academic Press
Electronic ISBN:
9780123946294
Print ISBN:
9780123942920

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