Main description:

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.

Contents:

1. In silico Identification and Characterization of Protein-Ligand Binding SitesDaniel Barry Roche and Liam James McGuffin2. Computational Modeling of Small Molecule Ligand Binding Interactions and AffinitiesMarino Convertino and Nikolay V. Dokholyan3. Binding Site Prediction of Proteins with Organic Compounds or Peptides Using GALAXY Web ServersLim Heo, Hasup Lee, Minkyung Baek, and Chaok Seok4. Rosetta and the Design of Ligand Binding Sites Rocco Moretti, Brian J. Bender, Brittany Allison, and Jens Meiler5. PocketOptimizer and the Design of Ligand Binding SitesAndre C. Stiel, Mehdi Nellen, and Birte Hoecker6. Proteus and the Design of Ligand Binding SitesSavvas Polydorides, Eleni Michael, David Mignon, Karen Druart, Georgios Archontis, and Thomas Simonson7. A Structure Based Design Protocol for Optimizing Combinatorial Protein LibrariesMark W. Lunt and Christopher D. Snow8. Combined and Iterative Use of Computational Design and Directed Evolution for Protein-Ligand Binding DesignMeng Wang and Huimin Zhao9. Improving Binding Affinity and Selectivity of Computationally DesignedLigand Binding Proteins Using ExperimentsChristine E. Tinberg and Sagar D. Khare10. Computational Design of Multinuclear Metalloproteins Using Unnatural Amino AcidsWilliam A. Hansen, Jeremy H. Mills, and Sagar D. Khare11. De Novo Design of Metalloproteins and Metalloenzymes in a Three-helix BundleJefferson S. Plegaria and Vincent L. Pecoraro12. Design of Light-Controlled Protein Conformations and FunctionsRyan S. Ritterson, Daniel Hoersch, Kyle A. Barlow, and Tanja Kortemme13. Computational Introduction of Catalytic Activity into ProteinsSteve J. Bertolani, Dylan Alexander Carlin, and Justin B. Siegel14. Generating High Accuracy Peptide Binding Data in High Throughput with Yeast Surface Display and SORTCERYLothar Reich, Sanjib Dutta, and Amy E. Keating15. Design of Specific Peptide-Protein RecognitionFan Zheng and Gevorg Grigoryan16. Computational Design of DNA-binding ProteinsSummer Thyme and Yifan Song17. Motif-driven Design of Protein-Protein InterfacesDaniel-Adriano Silva, Bruno E. Correia, and Erik Procko18. Computational Reprogramming of T Cell Antigen Receptor Binding PropertiesTimothy P. Riley, Nishant K. Singh, Brian G. Pierce, Brian M. Baker, and Zhiping Weng19. Computational Modeling of T Cell Receptor ComplexesTimothy P. Riley, Nishant K. Singh, Brian G. Pierce, Zhiping Weng, and Brian M. Baker20. Computational Design of Protein LinkersBrian Kuhlman, Tim Jacobs, and Tom Linskey21. Modeling of Protein-RNA Complex Structures Using Computational Docking MethodsBharat Madan, Joanna Kasprzak, Irina Tuszynska, Marcin Magnus, Krzysztof Szczepaniak, Wayne Dawson, and Janusz M. Bujnicki