In silico Identification and Characterization of Protein-Ligand Binding Sites -- Computational Modeling of Small Molecule Ligand Binding Interactions and Affinities -- Binding Site Prediction of Proteins with Organic Compounds or Peptides Using GALAXY Web Servers -- Rosetta and the Design of Ligand Binding Sites -- PocketOptimizer and the Design of Ligand Binding Sites -- Proteus and the Design of Ligand Binding Sites -- A Structure Based Design Protocol for Optimizing Combinatorial Protein Libraries -- Combined and Iterative Use of Computational Design and Directed Evolution for Protein-Ligand Binding Design -- Improving Binding Affinity and Selectivity of Computationally Designed Ligand Binding Proteins Using Experiments -- Computational Design of Multinuclear Metalloproteins Using Unnatural Amino Acids -- De Novo Design of Metalloproteins and Metalloenzymes in a Three-helix Bundle -- Design of Light-Controlled Protein Conformations and Functions -- Computational Introduction of Catalytic Activity into Proteins -- Generating High Accuracy Peptide Binding Data in High Throughput with Yeast Surface Display and SORTCERY -- Design of Specific Peptide-Protein Recognition -- Computational Design of DNA-binding Proteins -- Motif-driven Design of Protein-Protein Interfaces -- Computational Reprogramming of T Cell Antigen Receptor Binding Properties -- Computational Modeling of T Cell Receptor Complexes -- Computational Design of Protein Linkers -- Modeling of Protein-RNA Complex Structures Using Computational Docking Methods.

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.