Computational Analysis and Conformational Modeling for Protein Structure and Interaction

Protein structure and interactions underpin the molecular logic of life, driving essential processes such as signal transduction, molecular recognition, and catalysis. Insights into this domain are pivotal for elucidating biological mechanisms, advancing therapeutic discovery, and enabling the rational design of engineered proteins. Experimental approaches notably X-ray crystallography, NMR spectroscopy, and cryo-EM together with recent AI-driven tools such as AlphaFold3, ESMFold, and RoseTTAFold All-Atom, have transformed protein structure determination. Nonetheless, these methods often struggle to capture the atomistic conformational dynamics that govern protein interactions. Computational analysis and conformational modelling bridge this gap, offering robust frameworks to simulate dynamics, predict conformational transitions, and interrogate molecular interactions at exceptional resolution. This Reprint, drawn from the Special Issue on "Computational Analysis and Conformational Modeling of Protein Structure and Interaction," showcases cutting-edge research that extends the frontiers of structural biology, computational chemistry, and drug design. It highlights advances in modelling protein flexibility, exploring complex formation, integrating computational predictions with experimental validation, and harnessing AI for structure and interaction forecasting, collectively providing a timely resource for innovation in biotechnology and medicine.