Grid-based surface generalized Born model for calculation of electrostatic binding free energies
Fast and accurate calculation of solvation free energies is central to many applications, such
as rational drug design. In this study, we present a grid-based molecular surface …
as rational drug design. In this study, we present a grid-based molecular surface …
Accuracy comparison of generalized Born models in the calculation of electrostatic binding free energies
S Izadi, RC Harris, MO Fenley… - Journal of chemical …, 2018 - ACS Publications
The need for accurate yet efficient representation of the aqueous environment in
biomolecular modeling has led to the development of a variety of generalized Born (GB) …
biomolecular modeling has led to the development of a variety of generalized Born (GB) …
Protein–ligand electrostatic binding free energies from explicit and implicit solvation
Accurate yet efficient computational models of solvent environment are central for most
calculations that rely on atomistic modeling, such as prediction of protein–ligand binding …
calculations that rely on atomistic modeling, such as prediction of protein–ligand binding …
Multiscale generalized born modeling of ligand binding energies for virtual database screening
HY Liu, SZ Grinter, X Zou - The journal of physical chemistry B, 2009 - ACS Publications
Generalized Born (GB) models are widely used to study the electrostatic energetics of solute
molecules including proteins. Previous work demonstrates that GB models may produce …
molecules including proteins. Previous work demonstrates that GB models may produce …
Generalized born model with a simple smoothing function
Based on recent developments in generalized Born (GB) theory that employ rapid volume
integration schemes (MS Lee, FR Salabury, Jr., and CL Brooks III, J Chem Phys 2002, 116 …
integration schemes (MS Lee, FR Salabury, Jr., and CL Brooks III, J Chem Phys 2002, 116 …
Efficient computation of the total solvation energy of small molecules via the R6 generalized Born model
B Aguilar, AV Onufriev - Journal of chemical theory and …, 2012 - ACS Publications
Efficient and accurate methodologies to compute solvation free energies of small molecules
are relevant for many biological and industrial research areas including rational drug …
are relevant for many biological and industrial research areas including rational drug …
Efficient generalized Born models for Monte Carlo simulations
The Generalized Born Surface Area theory (GBSA) has become a popular method to model
the solvation of biomolecules. While efficient in the context of molecular dynamics …
the solvation of biomolecules. While efficient in the context of molecular dynamics …
Parameters for the generalized born model consistent with RESP atomic partial charge assignment protocol
Here we report a set of new parameters for the generalized Born (GB) model consistent with
the RESP atomic partial charge assignment protocol. Effective atomic radii and screen …
the RESP atomic partial charge assignment protocol. Effective atomic radii and screen …
Evaluation of generalized born model accuracy for absolute binding free energy calculations
F Zeller, M Zacharias - The Journal of Physical Chemistry B, 2014 - ACS Publications
Generalized Born (GB) implicit solvent models are widely used in molecular dynamics
simulations to evaluate the interactions of biomolecular complexes. The continuum …
simulations to evaluate the interactions of biomolecular complexes. The continuum …
Electrostatics of ligand binding: Parametrization of the generalized born model and comparison with the Poisson− Boltzmann approach
HY Liu, X Zou - The Journal of Physical Chemistry B, 2006 - ACS Publications
An accurate and fast evaluation of the electrostatics in ligand− protein interactions is crucial
for computer-aided drug design. The pairwise generalized Born (GB) model, a fast analytical …
for computer-aided drug design. The pairwise generalized Born (GB) model, a fast analytical …