Conclusions and Future Work

This thesis has presented a comprehensive exploration of the conformational dynamics of three distinct biomolecules: the hepatitis B virus (HBV) capsid assembly modulator AT130, the pertactin passenger domain, and the SARS-CoV-2 spike protein. Utilizing advanced simulation techniques and enhanced sampling, we have explored the complex behaviors of these biomolecules, each representing a unique facet of biological complexity. In the process, I also updated the open source parameterization tool, Force Field Toolkit (ffTK), to allow the use of the new \(\sigma \) -hole particle (LP) from CHARMM General Force Field (CGenFF) 4.0. Our investigations spanned different scales and complexities, demonstrating the versatility and applicability of simulations and enhanced sampling techniques in studying diverse biological systems.