Solvation Free Energy of and Solvent Mediated Force on Proteins
نویسندگان
چکیده
منابع مشابه
“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 کاملOn the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy.
Implicit solvent hydration free energy models are an important component of most modern computational methods aimed at protein structure prediction, binding affinity prediction, and modeling of conformational equilibria. The nonpolar component of the hydration free energy, consisting of a repulsive cavity term and an attractive van der Waals solute-solvent interaction term, is often modeled usi...
متن کاملPredicting Solvation Free Energies Using Parameter-Free Solvent Models.
We present a new approach for predicting solvation free energies in nonaqueous solvents. Utilizing the corresponding states principle, we estimate solvent Lennard-Jones parameters directly from their critical points. Combined with atomic solutes and the pressure corrected three-dimensional reference interaction site model (3D-RISM/PC+), the model gives accurate predictions for a wide range of n...
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 کاملAutomatic GROMACS topology generation and comparisons of force fields for solvation free energy calculations.
Free energy calculation has long been an important goal for molecular dynamics simulation and force field development, but historically it has been challenged by limited performance, accuracy, and creation of topologies for arbitrary small molecules. This has made it difficult to systematically compare different sets of parameters to improve existing force fields, but in the past few years seve...
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: Biophysical Journal
سال: 2009
ISSN: 0006-3495
DOI: 10.1016/j.bpj.2008.12.2898