Sun and coworkers made an extensive study of the entropy effects when this term is consider in MM/PB(GB)SA methods. From among all existing methodologies to estimate entropy, only two were selected, truncated normal mode analysis (truncated NMA) and interaction entropy (IE). Results based on minimized structures and MD simulations were exposed, including a dielectric constant sampling. In general, a synergy between IE calculations and MM/PB(GB)SA methods is argued, although dielectric constant is consider the only disadvantage. Interestingly, in terms of reprodicing the absolute binding free energy, the NME-MD based method showed the lowest deviations.
Sun and coworkers made an extensive study of the entropy effects when this term is consider in MM/PB(GB)SA methods. From among all existing methodologies to estimate entropy, only two were selected, truncated normal mode analysis (truncated NMA) and interaction entropy (IE). Results based on minimized structures and MD simulations were exposed, including a dielectric constant sampling. In general, a synergy between IE calculations and MM/PB(GB)SA methods is argued, although dielectric constant is consider the only disadvantage. Interestingly, in terms of reprodicing the absolute binding free energy, the NME-MD based method showed the lowest deviations.