Classical molecular electrostatics: Recognition of ligands in proteins and the vibrational stark effect

Article Abstract:

A study shows that classical electrostatistics describes the quantitative description of, both the binding of the diatomic ligands XO (X= C. N, O) to the heme group in myoglobin and the dependence of their vibrational frequencies upon an external field by classical electrolysis. It is suggested that ligand binding occurs via an electrostatic bond, a generalization of the standard ionic bond to include induction, and that classical electrostatics can replace quantum mechanics for a considerable simplification of some complex problems.

Myoglobin, Chemical properties, Stark effect, Report

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Electrostatics of ligand binding: Parametrization of the generalized Born model and comparison with the Poisson-Boltzmann approach

Article Abstract:

The Poisson-Boltzmann (PB) approach is used as a reference to optimize the generalized Born (GB) model for the studies of ligand-protein interactions. The calculation of the electrostatic component of free energies of ligand binding with the help of GB and PB methods and also the parametrization of the descreening parameters in the Hawkins, Cramer and Truhlar version of the GB model.

Electrostatics, Transport theory, Poisson processes

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Pairwise GB/SA scoring function for structure-based drug design

Article Abstract:

A pairwise Born radius approximation is used to present a fast algorithm for ligand-protein binding affinity calculations. This procedure is developed to account for the low-dielectric region that might form between the ligand and the receptor during docking processes and also used to screen a large database directly.

Chemistry, Physical and theoretical, Physical chemistry, Binding proteins

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