Molecular volumes and surfaces of biomacromolecules via GEPOL: A fast and efficient algorithm

Silla, Estanislao; Villar, Félix; Nilsson, Ola; Pascual-Ahuir, Juan-Luis; Tapia, O.

doi:10.1016/0263-7855(90)80059-o

Cited by 100 publications

(47 citation statements)

References 16 publications

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“…The coordination number, z, is set to 10. Polarizable Continuum Model (PCM) [52] with the GEnerating POLyhedra (GEPOL) algorithm [53] was used to calculate the r and q in the UNIQUAC model after the ILs structures being optimized by Density Functional Theory (DFT) [54]. DFT based on a hypothesis that the electron density distribution completely characterizes the ground state of a many electron system is a most popular method for calculating the electronic structure of atoms, molecules, liquids, solids, and plasmas.…”

Section: Thermodynamic Modelsmentioning

confidence: 99%

Liquid–liquid equilibria for ternary mixtures of water + 2-propanol + 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ionic liquids at 298.15 K

Liu

Zhang

et al. 2016

Fluid Phase Equilibria

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Section: Thermodynamic Modelsmentioning

confidence: 99%

Liquid–liquid equilibria for ternary mixtures of water + 2-propanol + 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ionic liquids at 298.15 K

Liu

Zhang

et al. 2016

Fluid Phase Equilibria

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“…[10][11][12] In this method, the solute is placed inside a cavity built, in general, as a set of interlocking spheres centered on solute atoms. [13][14][15] The cavity surface is divided into small tesserae, and the polarization of the solvent is represented by surface charges placed on their center. Although PCM provides an accurate way of calculating physical properties of solvated systems, it has a major drawback:…”

Section: Introductionmentioning

confidence: 99%

Multigrid-Based Methodology for Implicit Solvation Models in Periodic DFT

García-Ratés

López

2016

J. Chem. Theory Comput.

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Continuum solvation models have become a widespread approach for the study of environmental effects in Density Functional Theory (DFT) methods. Adding solvation contributions mainly relies on the solution of the Generalized Poisson Equation (GPE) governing the behavior of the electrostatic potential of a system. Although multigrid methods are especially appropriate for the solution of partial differential equations, up to now, their use is not much extended in DFT-based codes because of their high memory requirements. In this Article, we report the implementation of an accelerated multigrid solver-based approach for the treatment of solvation effects in the Vienna ab initio Simulation Package (VASP). The stated implicit solvation model, named VASP-MGCM (VASP-Multigrid Continuum Model), uses an efficient and transferable algorithm for the product of sparse matrices that highly outperforms serial multigrid solvers. The calculated solvation free energies for a set of molecules, including neutral and ionic species, as well as adsorbed molecules on metallic surfaces, agree with experimental data and with simulation results obtained with other continuum models.

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“…The weighted root mean square deviation (RMSD) of the modeled protein was calculated using combinatorial extension (CE) algorithm [26] . Solvent accessibility was measured using the program GEPOL [27] . The computed structure of the 1A-adrenoceptor obtained was refined by energy minimization with CHARMM force field until the energy showed stability in sequential repetition [28] .…”

Section: Methodsmentioning

confidence: 99%

In silico Modeling of α1A-Adrenoceptor: Interaction of its Normal and Mutated Active Sites with Noradrenaline as well as its Agonist and Antagonist

Vijayan¹,

Subbarao²,

Mallick³

2007

American J. of Biochemistry and Biotechnology

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Noradrenaline, like most other neurotransmitters, acts through various adrenoceptor subtypes. The structure and active site of adrenoceptors for the binding of noradrenaline were unknown, however, such information are crucial for understanding the molecular mechanism of action of neurotransmitters, including noradrenaline, in health and disease as well as for drug designing. In this in silico study, we modeled the 1A-adrenoceptor; a G protein coupled receptor and defined its active site. Further, molecular docking and interaction of noradrenaline and its agonist as well as antagonist with the so defined active site of the receptor was studied before and after in silico site directed mutation of several amino acid residues forming the active site. Our results indicate that the ARG166 is the most crucial residue for binding of noradrenaline and methoxamine to 1A-adrenoceptor and ILE178 is the most important residue for binding of prazosin to it. Thus, the observations provide new insights into the structure function relationship of 1A-adrenoceptor. A significant finding of this study is that the same residue of the active site may not be necessary for binding of a receptor with its natural ligand and its pharmacologically active known agonist and antagonist.

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Molecular volumes and surfaces of biomacromolecules via GEPOL: A fast and efficient algorithm

Cited by 100 publications

References 16 publications

Liquid–liquid equilibria for ternary mixtures of water + 2-propanol + 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ionic liquids at 298.15 K

Liquid–liquid equilibria for ternary mixtures of water + 2-propanol + 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ionic liquids at 298.15 K

Multigrid-Based Methodology for Implicit Solvation Models in Periodic DFT

In silico Modeling of α1A-Adrenoceptor: Interaction of its Normal and Mutated Active Sites with Noradrenaline as well as its Agonist and Antagonist

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