Protein-Protein Docking Methods and Protocols

This volume covers a wide array of topics on protein-protein docking ranging from the fundamentals of the method and its recent developments to docking tools and examples of protein-protein docking applications. The chapters in this book are organized into four parts. Part One looks at the fundamentals of protein-protein docking such as rigid and flexible docking, and sampling and scoring in protein-protein docking. Part Two focuses on the latest advancements made in the field such as how the protein backbone flexibility is treated. Part Three explores practical applications of protein-protein docking tools and databases, with emphasis on software for predicting binding free energy of protein-protein complexes and their mutants. Part Four talks about protein-protein docking approaches to different systems, and their challenges and strategies of molecular docking of intrinsically disordered proteins. 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.

Cutting-edge and thorough, Protein-Protein Docking: Methods and Protocols is a valuable resource for structural biologists, bioinformaticians, molecular modelers, and medicinal chemists looking to learn more about this important field.

Docking Foundations: From Rigid to Flexible Docking.- Sampling and Scoring in Protein-Protein Docking.- Free-Docking and Template-Based Docking: Physics Versus Knowledge-Based Docking.- Approaches to Backbone Flexibility in Protein-Protein Docking.- From Multiple Protein Docking to Protein-Protein Docking at Interactome Level.- Molecular Dynamics Simulations in Protein-Protein Docking.- Machine Learning Methods in Protein-Protein Docking.- Software and Databases for Protein-Protein Docking.- Software for Predicting Binding Free Energy of Protein–Protein Complexes and Their Mutants.- Assessment of Protein-Protein Docking Models using Deep Learning.- Molecular Docking of Intrinsically Disordered Proteins: Challenges and Strategies.- Challenges of Protein-Protein Docking of the Membrane Proteins.- Assessing Protein-Protein Docking Protocols: Case Studies of G Protein-Coupled Receptor Interactions.- Protein-Protein Docking Approach to GPCR Oligomerization.- Refinement of Docked Protein-Protein Complexes using Repulsive Scaling Replica Exchange Simulations.- Exploiting the Role of Features for Antigens-Antibodies Interaction Site Prediction.- Computational Methods to Target Protein-Protein Interactions.- In Silico Design, Synthesis, and Evaluation of PROTAC against Hematopoietic Prostaglandin D Synthase.