We study how protein conformational dynamics shape molecular function, focusing on the effects of mutations, post-translational modifications, and molecular binding on conformational ensembles, long-range allosteric communication, molecular recognition, and the stability of functional complexes. Combining molecular simulation, dynamical networks, and machine learning, we develop and evaluate methods for conformational sampling, conformation generation, and allosteric pathway analysis. Our goal is to reveal the molecular mechanisms of protein regulation and provide a theoretical basis for intervention strategies.
