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Computational Design of Ligand Binding Proteins, 1st ed. 2016 Methods in Molecular Biology Series, Vol. 1414

Langue : Anglais
Couverture de l’ouvrage Computational Design of Ligand Binding Proteins

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.


1. In silico Identification and Characterization of Protein-Ligand Binding Sites
Daniel Barry Roche and Liam James McGuffin
2. Computational Modeling of Small Molecule Ligand Binding Interactions and Affinities
Marino Convertino and Nikolay V. Dokholyan
3. Binding Site Prediction of Proteins with Organic Compounds or Peptides Using GALAXY Web Servers
Lim Heo, Hasup Lee, Minkyung Baek, and Chaok Seok
4. Rosetta and the Design of Ligand Binding Sites Rocco Moretti, Brian J. Bender, Brittany Allison, and Jens Meiler
5. PocketOptimizer and the Design of Ligand Binding Sites
Andre C. Stiel, Mehdi Nellen, and Birte Höcker
6. Proteus and the Design of Ligand Binding Sites
Savvas Polydorides, Eleni Michael, David Mignon, Karen Druart, Georgios Archontis, and Thomas Simonson
7. A Structure Based Design Protocol for Optimizing Combinatorial Protein Libraries
Mark W. Lunt and Christopher D. Snow
8. Combined and Iterative Use of Computational Design and Directed Evolution for Protein-Ligand Binding Design
Meng Wang and Huimin Zhao
9. Improving Binding Affinity and Selectivity of Computationally Designed
Ligand Binding Proteins Using Experiments
Christine E. Tinberg and Sagar D. Khare
10. Computational Design of Multinuclear Metalloproteins Using Unnatural Amino Acids
William A. Hansen, Jeremy H. Mills, and Sagar D. Khare
11. De Novo Design of Metalloproteins and Metalloenzymes in a Three-helix Bundle
Jefferson S. Plegaria and Vincent L. Pecoraro
12. Design of Light-Controlled Protein Conformations and Functions
Ryan S. Ritterson, Daniel Hoersch, Kyle A. Barlow, and Tanja Kortemme
13. Computational Introduction of Catalytic Activity into Proteins
Steve J. Bertolani, Dylan Alexander Carlin, and Justin B. Siegel
14. Generating High Accuracy Peptide Binding Data in High Throughput with Yeast Surface Display and SORTCERY
Lothar Reich, Sanjib Dutta, and Amy E. Keating
15. Design of Specific Peptide-Protein Recognition
Fan Zheng and Gevorg Grigoryan
16. Computational Design of DNA-binding Proteins
Summer Thyme and Yifan Song
17. Motif-driven Design of Protein-Protein Interfaces
Daniel-Adriano Silva, Bruno E. Correia, and Erik Procko
18. Computational Reprogramming of T Cell Antigen Receptor Binding Properties
Timothy P. Riley, Nishant K. Singh, Brian G. Pierce, Brian M. Baker, and Zhiping Weng
19. Computational Modeling of T Cell Receptor Complexes
Timothy P. Riley, Nishant K. Singh, Brian G. Pierce, Zhiping Weng, and Brian M. Baker
20. Computational Design of Protein Linkers
Brian Kuhlman, Tim Jacobs, and Tom Linskey
21. Modeling of Protein-RNA Complex Structures Using Computational Docking Methods
Bharat Madan, Joanna Kasprzak, Irina Tuszynska, Marcin Magnus, Krzysztof Szczepaniak, Wayne Dawson, and Janusz M. Bujnicki

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

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Date de parution :

Ouvrage de 375 p.

17.8x25.4 cm

Disponible chez l'éditeur (délai d'approvisionnement : 15 jours).

Prix indicatif 105,49 €

Ajouter au panier