Protein Supersecondary Structures Methods and Protocols

This new edition delves into the latest developments in the field and new techniques used to study secondary and supersecondary structures (SSS) in proteins. Beyond the tremendous advances in the field from the AI-based AlphaFold algorithm, researchers continue to untangle how specific structures and protein folds come to be, and these chapters contain numerous techniques to further pursue this study. Written for the highly successful Methods in Molecular Biology series, chapters contain the kind of detailed implementation advice needed to ensure effective results in the lab. 

Authoritative and practical, Protein Supersecondary Structures: Methods and Protocols, Third Edition serves as a valuable resource for researchers exploring the relationship between amino acids sequences and protein structures, the evolution of proteins, and the dynamics of protein formation.

Recent Advances in Computational Prediction of Secondary and Supersecondary Structures from Protein Sequences.- Complementary Packing of a-Helices Revisited.- The 3D Invariant Positioning for Protein Molecules / Molecular Complexes with Matching Subunits.- Beta Sandwich-Like Folds: Sequences, Contacts, Classification of Invariant Substructures and Beta Sandwich Protein Grammar.- Conformational Variability Prediction of Influenza Virus Hemagglutinins with Amino Acid Mutations Using Supersecondary Structure Code.- Statistical Analysis of Walker-A Motif-Containing ß-a-ß Supersecondary Structures in the Protein Data Bank.- Discovery and Analysis of Repeat and Low-Complexity Architectures in Proteins and Their Conserved Evolutionary Relationships Using Self-Homology Dot Plots.- Advances in Prediction of Post-Translational Modification Sites Known to Localize in Protein Supersecondary Structures.- Prediction of the Stability of Protein Substructures Using AI/ML Techniques.- Leveraging Artificial Intelligence in GPCR Activation Studies: Computational Prediction Methods as Key Drivers of Knowledge.- Techniques For Bioinformatic Applications in Protein Dynamics.- Quantifying Protein-Nucleic Acid Interactions for Engineering Useful CRISPR-Cas9 Genome-Editing Variants.- Building Up Functional Coiled Coil-Based Supramolecular Assemblies for Biomedical and Biotechnological Applications.- Mean-Field Coupling Between Local Interactions in Proteins in Relation to Chirality, Secondary and Supersecondary Structure Formation, and Allostery.- Graph-Theoretical Prediction and Analysis of Biologically Relevant Substructures in an Open and Closed Conformation of Respiratory Complex I.- The Role of Protonation in the PfMATE Transporter Protein Structural Transitions.- Secondary Structure Detection and Structure Modeling for Cryo-EM.- Hierarchical Analysis of Protein Structures: From Secondary Structures to Protein Units and Domains.- Ig or Not Ig? That is the Question: The Nucleating Supersecondary Structure of the Ig-Fold and the Extended Ig Universe.