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Implicit Solvation Models - Welcome to the Center for Molecular 隐式溶剂模型-欢迎中心分子
Introduction to Molecular Biophysics Implicit Solvation Models Xiaolin Cheng UT/ORNL Center for Molecular Biophysics 02/18/2008 Water is important Water Molecule Structure Explicit Water Models Explicit Water Models Explicit Water Model Examples Explicit Water Models Explicit Water Models Further Readings Implicit Solvation Models Implicit Solvation Models Implicit Solvation Models Implicit Solvation Models Nonpolar Solvation Nonpolar Solvation Nonpolar Solvation Polar Solvation Polar Solvation Polar Solvation Poisson-Boltzmann Theory Numerical Solution of PB Numerical Solution of PB Delphi Delphi APBS APBS Diverse Applications Diverse Applications Diverse Applications Diverse Applications Diverse Applications Diverse Applications Diverse Applications Practical Considerations More on pKa Calculations More on pKa Calculations Generalized Born Model Generalized Born Model Microscopic Definition of Born Radii Calculation of Born Radii Generalized Born Model Limitations of Implicit Solvation Models The hydrophobic effect this surface area pertains to the solute, while the hydrophobic effect is entropic in nature and occurs on the side of the solvent. Viscosity water molecules by randomly colliding and impeding the motion of solutes - makes sampling of configurations and phase space faster; misleading kinetics results; using Langevin dynamics with a damping constant Coupling between nonpolar and polar terms Recent discussion see, J. Dzubiella et al. J. Chem. Phys. 2006 Pay attention to parameterization details Over-stabilized salt-bridge Limitations of Implicit Solvation Models Hydrogen-bonds with water The average energetic contribution of protein-water hydrogen bonds may be reproduced with an implicit solvent. However, the directionality of these hydrogen bonds will be missing. 1. solvent transfer energies, binding energies, pKa shifts, solvent forces, surface potentials and effective dielectric constants; 2. Protein-protein, protein-DNA, protein-ligand interac
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