Stretching DNA to Quantify Non-Specific Binding by the Lambda Repressor (ci)

Abstract

Traditional molecular dynamics techniques can compute free energy differences between well defined states, but currently they cannot consistently estimate the full contribution of the solvent. In parallel, considerable efforts are being devoted to the development of polarizable force fields. Despite their solid theoretical foundation, these methods have yet to reach their full potential and, equally important, justify their computational cost. On the other hand, there is an urgent need to improve the predictive power of physically based empirical potentials to better understand the molecular basis of protein interactions and function, and expedite molecular engineering and drug design. Here, we propose a comprehensive and scalable approach to include polarization/dielectric effects that uses