Implicit solvent methods for free energy estimation
نویسندگان
چکیده
منابع مشابه
Electrostatic free energy and its variations in implicit solvent models.
A mean-field approach to the electrostatics for solutes in electrolyte solution is revisited and rigorously justified. In this approach, an electrostatic free energy functional is constructed that depends solely on the local ionic concentrations. The unique set of such concentrations that minimize this free energy are given by the usual Boltzmann distributions through the electrostatic potentia...
متن کاملExtension of the free energy workflow FEW towards implicit solvent/implicit membrane MM-PBSA calculations.
BACKGROUND The number of high-resolution structures of pharmacologically relevant membrane proteins has been strongly increasing. This makes computing relative affinities of chemically similar compounds binding to a membrane protein possible in order to guide decision making in drug design. However, the preparation step of such calculations is time-consuming and complex. METHODS We extended t...
متن کاملMinimization of Electrostatic Free Energy and the Poisson-Boltzmann Equation for Molecular Solvation with Implicit Solvent
In an implicit-solvent description of the solvation of charged molecules (solutes), the electrostatic free energy is a functional of concentrations of ions in the solvent. The charge density is determined by such concentrations together with the point charges of the solute atoms, and the electrostatic potential is determined by the Poisson equation with a variable dielectric coefficient. Such a...
متن کامل“Martinizing” the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins
Solvation is a fundamental driving force in many biological processes including biomolecular recognition and self-assembly, not to mention protein folding, dynamics, and function. The variational implicit solvent method (VISM) is a theoretical tool currently developed and optimized to estimate solvation free energies for systems of very complex topology, such as biomolecules. VISM's theoretical...
متن کاملRecent advances in implicit solvent-based methods for biomolecular simulations.
Implicit solvent-based methods play an increasingly important role in molecular modeling of biomolecular structure and dynamics. Recent methodological developments have mainly focused on the extension of the generalized Born (GB) formalism for variable dielectric environments and accurate treatment of nonpolar solvation. Extensive efforts in parameterization of GB models and implicit solvent fo...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: European Journal of Medicinal Chemistry
سال: 2015
ISSN: 0223-5234
DOI: 10.1016/j.ejmech.2014.08.064