Visualization and Analysis of Protein Structures with LiteMol Suite -- Comparative Protein Structure Analysis with Bio3D-Web -- Using DALI for Protein Structure Comparison -- Assessing Protein Function through Structural Similarities with CATH -- Protein Thermal Stability Engineering using HoTMuSiC -- Contact Area-Based Structural Analysis of Proteins and their Complexes using CAD-Score -- A Comprehensive Computational Platform to Guide Drug Development using Graph-Based Signature Methods -- Systematic Exploration of Binding Modes of Ligands on Drug Targets -- Using MemBlob to Analyze Transmembrane Regions Based on Cryo-EM Maps -- Structural Characterization of Protein-Protein Interactions with pyDockSAXS -- Protein-Protein Modeling using Cryo-EM Restraints -- Modeling of Multimolecular Complexes -- Biological Assembly Comparison with VAST+ -- BioMagResBank (BMRB) as a Resource for Structural Biology -- Integrating Molecular Simulation and Experimental Data: A Bayesian/Maximum Entropy Reweighting Approach -- Evaluation and Selection of Dynamic Protein Structural Ensembles with CoNSEnsX+.

This volume looks at the latest techniques used to perform comparative structure analyses, and predict and evaluate protein-ligand interactions. The chapters in this book cover tools and servers such as LiteMol; Bio3D-Web; DALI; CATH; HoTMuSiC, a contact-base protein structure analysis tool known as CAD-Score; PyDockSaxs and HADDOCK; CombDock and DockStar; the BioMagResBank database; as well as BME and CoNSEnsX+. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible computational protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Structural Bioinformatics: Methods and Protocols is a practical guide for researchers to learn more about the aforementioned tools to further enhance their studies in the growing field of structural bioinformatics. Chapter 13 is open access under a CC-BY 4.0 license via link.springer.com.