Computational Design of Ligand Binding Proteins

  • Barry L. Stoddard

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

Table of contents

  1. Front Matter
    Pages i-xvi
  2. Daniel Barry Roche, Liam James McGuffin
    Pages 1-21
  3. Rocco Moretti, Brian J. Bender, Brittany Allison, Jens Meiler
    Pages 47-62
  4. Andre C. Stiel, Mehdi Nellen, Birte Höcker
    Pages 63-75
  5. Savvas Polydorides, Eleni Michael, David Mignon, Karen Druart, Georgios Archontis, Thomas Simonson
    Pages 77-97
  6. William A. Hansen, Jeremy H. Mills, Sagar D. Khare
    Pages 173-185
  7. Jefferson S. Plegaria, Vincent L. Pecoraro
    Pages 187-196
  8. Ryan S. Ritterson, Daniel Hoersch, Kyle A. Barlow, Tanja Kortemme
    Pages 197-211
  9. Steve J. Bertolani, Dylan Alexander Carlin, Justin B. Siegel
    Pages 213-231
  10. Lothar “Luther” Reich, Sanjib Dutta, Amy E. Keating
    Pages 233-247
  11. Fan Zheng, Gevorg Grigoryan
    Pages 249-263
  12. Summer Thyme, Yifan Song
    Pages 265-283
  13. Daniel-Adriano Silva, Bruno E. Correia, Erik Procko
    Pages 285-304
  14. Timothy P. Riley, Nishant K. Singh, Brian G. Pierce, Brian M. Baker, Zhiping Weng
    Pages 305-318
  15. Timothy P. Riley, Nishant K. Singh, Brian G. Pierce, Zhiping Weng, Brian M. Baker
    Pages 319-340
  16. Brian Kuhlman, Tim Jacobs, Tom Linskey
    Pages 341-351
  17. Bharat Madan, Joanna M. Kasprzak, Irina Tuszynska, Marcin Magnus, Krzysztof Szczepaniak, Wayne K. Dawson et al.
    Pages 353-372
  18. Back Matter
    Pages 373-375

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 on troubleshooting and avoiding known pitfalls.


ligand-binding proteins individual docked solutions ROSETTA protein engineering metal-binding proteins light-induced ligand binding proteins

Editors and affiliations

  • Barry L. Stoddard
    • 1
  1. 1.Division of Basic SciencesFred Hutchinson Cancer Research CenSeattleUSA

Bibliographic information

  • DOI
  • Copyright Information Springer Science+Business Media New York 2016
  • Publisher Name Humana Press, New York, NY
  • eBook Packages Springer Protocols
  • Print ISBN 978-1-4939-3567-3
  • Online ISBN 978-1-4939-3569-7
  • Series Print ISSN 1064-3745
  • Series Online ISSN 1940-6029
  • Buy this book on publisher's site
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