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Computational Design of Ligand Binding Proteins

  • Book
  • © 2016

Overview

Editors:
  1. Barry L. Stoddard

    1. Division of Basic Sciences, Fred Hutchinson Cancer Research Cen, Seattle, USA

    View editor publications

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  • Includes cutting-edge methods and protocols
  • Provide step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 1414)

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About this book

This volume provides a collection of protocols and approaches for the creation of novel ligand binding proteins, compiled and described by many of today's leaders in the field of protein engineering. Chapters focus on modeling protein ligand binding sites, accurate modeling of protein-ligand conformational sampling, scoring of individual docked solutions, structure-based design program such as ROSETTA, protein engineering, and additional methodological approaches. Examples of applications include the design of metal-binding proteins and light-induced ligand binding proteins, the creation of binding proteins that also display catalytic activity, and the binding of larger peptide, protein, DNA and RNA ligands. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips ontroubleshooting and avoiding known pitfalls.


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Table of contents (21 protocols)

  1. Front Matter

    Pages i-xvi
    Download chapter PDF

  2. In silico Identification and Characterization of Protein-Ligand Binding Sites

    • Daniel Barry Roche, Liam James McGuffin
    Pages 1-21

  3. Computational Modeling of Small Molecule Ligand Binding Interactions and Affinities

    • Marino Convertino, Nikolay V. Dokholyan
    Pages 23-32

  4. Binding Site Prediction of Proteins with Organic Compounds or Peptides Using GALAXY Web Servers

    • Lim Heo, Hasup Lee, Minkyung Baek, Chaok Seok
    Pages 33-45

  5. Rosetta and the Design of Ligand Binding Sites

    • Rocco Moretti, Brian J. Bender, Brittany Allison, Jens Meiler
    Pages 47-62

  6. PocketOptimizer and the Design of Ligand Binding Sites

    • Andre C. Stiel, Mehdi Nellen, Birte Höcker
    Pages 63-75

  7. Proteus and the Design of Ligand Binding Sites

    • Savvas Polydorides, Eleni Michael, David Mignon, Karen Druart, Georgios Archontis, Thomas Simonson
    Pages 77-97

  8. A Structure-Based Design Protocol for Optimizing Combinatorial Protein Libraries

    • Mark W. Lunt, Christopher D. Snow
    Pages 99-138

  9. Combined and Iterative Use of Computational Design and Directed Evolution for Protein–Ligand Binding Design

    • Meng Wang, Huimin Zhao
    Pages 139-153

  10. Improving Binding Affinity and Selectivity of Computationally Designed Ligand-Binding Proteins Using Experiments

    • Christine E. Tinberg, Sagar D. Khare
    Pages 155-171

  11. Computational Design of Multinuclear Metalloproteins Using Unnatural Amino Acids

    • William A. Hansen, Jeremy H. Mills, Sagar D. Khare
    Pages 173-185

  12. De Novo Design of Metalloproteins and Metalloenzymes in a Three-Helix Bundle

    • Jefferson S. Plegaria, Vincent L. Pecoraro
    Pages 187-196

  13. Design of Light-Controlled Protein Conformations and Functions

    • Ryan S. Ritterson, Daniel Hoersch, Kyle A. Barlow, Tanja Kortemme
    Pages 197-211

  14. Computational Introduction of Catalytic Activity into Proteins

    • Steve J. Bertolani, Dylan Alexander Carlin, Justin B. Siegel
    Pages 213-231

  15. Generating High-Accuracy Peptide-Binding Data in High Throughput with Yeast Surface Display and SORTCERY

    • Lothar “Luther” Reich, Sanjib Dutta, Amy E. Keating
    Pages 233-247

  16. Design of Specific Peptide–Protein Recognition

    • Fan Zheng, Gevorg Grigoryan
    Pages 249-263

  17. Computational Design of DNA-Binding Proteins

    • Summer Thyme, Yifan Song
    Pages 265-283

  18. Motif-Driven Design of Protein–Protein Interfaces

    • Daniel-Adriano Silva, Bruno E. Correia, Erik Procko
    Pages 285-304

  19. Computational Reprogramming of T Cell Antigen Receptor Binding Properties

    • Timothy P. Riley, Nishant K. Singh, Brian G. Pierce, Brian M. Baker, Zhiping Weng
    Pages 305-318

  20. Computational Modeling of T Cell Receptor Complexes

    • Timothy P. Riley, Nishant K. Singh, Brian G. Pierce, Zhiping Weng, Brian M. Baker
    Pages 319-340
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Editors and Affiliations

  • Division of Basic Sciences, Fred Hutchinson Cancer Research Cen, Seattle, USA

    Barry L. Stoddard

Bibliographic Information

  • Book Title: Computational Design of Ligand Binding Proteins

  • Editors: Barry L. Stoddard

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-3569-7

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2016

  • Hardcover ISBN: 978-1-4939-3567-3Published: 20 April 2016

  • Softcover ISBN: 978-1-4939-8080-2Published: 21 April 2018

  • eBook ISBN: 978-1-4939-3569-7Published: 19 April 2016

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XVI, 375

  • Number of Illustrations: 18 b/w illustrations, 76 illustrations in colour

  • Topics: Protein Science, Protein-Ligand Interactions

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