Computational Design of Ligand Binding Proteins (eBook, PDF)

Redaktion: Stoddard, Barry L.

• Format: PDF

Produktbeschreibung

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.

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Produktdetails

• Verlag: Springer New York
• Seitenzahl: 375
• Erscheinungstermin: 19. April 2016
• Englisch
• ISBN-13: 9781493935697
• Artikelnr.: 64701809

Inhaltsangabe

In silico Identification and Characterization of Protein-Ligand BindingSites.- Computational Modeling of Small Molecule Ligand Binding Interactionsand Affinities.- Binding Site Prediction of Proteins with Organic Compounds orPeptides Using GALAXY Web Servers.- Rosetta and the Design of Ligand Binding Sites.-PocketOptimizer and the Design of Ligand Binding Sites.- Proteus and the Designof Ligand Binding Sites.- A Structure Based Design Protocol for OptimizingCombinatorial Protein Libraries.- Combined and Iterative Use of ComputationalDesign and Directed Evolution for Protein-Ligand Binding Design.- ImprovingBinding Affinity and Selectivity of Computationally Designed Ligand BindingProteins Using Experiments.- Computational Design of MultinuclearMetalloproteins Using Unnatural Amino Acids.- De Novo Design ofMetalloproteins and Metalloenzymes in a Three-helix Bundle.- Design ofLight-Controlled Protein Conformations and Functions.- ComputationalIntroduction of Catalytic Activity into Proteins.- Generating High AccuracyPeptide Binding Data in High Throughput with Yeast Surface Display andSORTCERY.- Design of Specific Peptide-Protein Recognition.- Computational Designof DNA-binding Proteins.- Motif-driven Design of Protein-Protein Interfaces.- ComputationalReprogramming of T Cell Antigen Receptor Binding Properties.- ComputationalModeling of T Cell Receptor Complexes.- Computational Design of ProteinLinkers.- Modeling of Protein-RNA Complex Structures Using ComputationalDocking Methods.