Including implicit solvation in the bond capacity polarization model
نویسندگان
چکیده
منابع مشابه
The AGBNP2 Implicit Solvation Model.
The AGBNP2 implicit solvent model, an evolution of the Analytical Generalized Born plus Non-Polar (AGBNP) model we have previously reported, is presented with the aim of modeling hydration effects beyond those described by conventional continuum dielectric representations. A new empirical hydration free energy component based on a procedure to locate and score hydration sites on the solute surf...
متن کاملKECSA-Movable Type Implicit Solvation Model (KMTISM)
Computation of the solvation free energy for chemical and biological processes has long been of significant interest. The key challenges to effective solvation modeling center on the choice of potential function and configurational sampling. Herein, an energy sampling approach termed the “Movable Type” (MT) method, and a statistical energy function for solvation modeling, “Knowledge-based and E...
متن کاملDiscrimination of the native from misfolded protein models with an energy function including implicit solvation.
An essential requirement for theoretical protein structure prediction is an energy function that can discriminate the native from non-native protein conformations. To date most of the energy functions used for this purpose have been extracted from a statistical analysis of the protein structure database, without explicit reference to the physical interactions responsible for protein stability. ...
متن کاملDomain decomposition for implicit solvation models.
This article is the first of a series of papers dealing with domain decomposition algorithms for implicit solvent models. We show that, in the framework of the COSMO model, with van der Waals molecular cavities and classical charge distributions, the electrostatic energy contribution to the solvation energy, usually computed by solving an integral equation on the whole surface of the molecular ...
متن کاملHydrogen Bond Kinetics in the Solvation Shell of a Polypeptide
Analysis of a series of molecular dynamics simulations reveals that the kinetics of breaking and forming water-water hydrogen bonds is slower in the first solvation shell of a 16-residue polypeptide than in bulk water. The correlation time of hydrogen bonds persists significantly longer near hydrophobic groups than in bulk water. Hydrogen bonds are found to be stronger in the solvation shell of...
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: The Journal of Chemical Physics
سال: 2019
ISSN: 0021-9606,1089-7690
DOI: 10.1063/1.5120873