Cargando…

A new set of atomic radii for accurate estimation of solvation free energy by Poisson–Boltzmann solvent model

The Poisson–Boltzmann implicit solvent (PB) is widely used to estimate the solvation free energies of biomolecules in molecular simulations. An optimized set of atomic radii (PB radii) is an important parameter for PB calculations, which determines the distribution of dielectric constants around the...

Descripción completa

Detalles Bibliográficos
Autores principales:	Yamagishi, Junya, Okimoto, Noriaki, Morimoto, Gentaro, Taiji, Makoto
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BlackWell Publishing Ltd 2014
Materias:	Full Papers
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263261/ https://www.ncbi.nlm.nih.gov/pubmed/25220475 http://dx.doi.org/10.1002/jcc.23728

Ejemplares similares

Variational Implicit Solvation with Poisson–Boltzmann Theory
por: Zhou, Shenggao, et al.
Publicado: (2014)

Poisson–Boltzmann versus Size-Modified Poisson–Boltzmann Electrostatics Applied to Lipid Bilayers
por: Wang, Nuo, et al.
Publicado: (2014)

PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson–Boltzmann treatment of macromolecule electrostatics
por: Azuara, Cyril, et al.
Publicado: (2006)

Problems of Robustness in Poisson–Boltzmann Binding Free Energies
por: Harris, Robert C., et al.
Publicado: (2015)

A discontinuous Poisson–Boltzmann equation with interfacial jump: homogenisation and residual error estimate
por: Fellner, Klemens, et al.
Publicado: (2015)

Drug binding dynamics of the dimeric SARS-CoV-2 main protease, determined by molecular dynamics simulation
por: Komatsu, Teruhisa S., et al.
Publicado: (2020)

An Adaptive Fast Multipole Boundary Element Method for Poisson−Boltzmann Electrostatics
por: Lu, Benzhuo, et al.
Publicado: (2009)

Review and Modification of Entropy Modeling for Steric Effects in the Poisson-Boltzmann Equation
por: Horng, Tzyy-Leng
Publicado: (2020)

Modeling Microtubule Counterion Distributions and Conductivity Using the Poisson-Boltzmann Equation
por: Eakins, Boden B., et al.
Publicado: (2021)

High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations
por: Okimoto, Noriaki, et al.
Publicado: (2009)

Large-scale all-atom molecular dynamics alanine-scanning of IAPP octapeptides provides insights into the molecular determinants of amyloidogenicity
por: Tambi, Richa, et al.
Publicado: (2019)

Contact pairs of RNA with magnesium ions-electrostatics beyond the Poisson-Boltzmann equation
por: Fingerhut, Benjamin Philipp, et al.
Publicado: (2021)

Accurate lineshape spectroscopy and the Boltzmann constant
por: Truong, G.-W., et al.
Publicado: (2015)

Exploring a coarse-grained distributive strategy for finite-difference Poisson–Boltzmann calculations
por: Hsieh, Meng-Juei, et al.
Publicado: (2010)

A Combined MPI-CUDA Parallel Solution of Linear and Nonlinear Poisson-Boltzmann Equation
por: Colmenares, José, et al.
Publicado: (2014)

Arbitrary-Shape Dielectric Particles Interacting in the Linearized Poisson–Boltzmann Framework: An Analytical Treatment
por: Siryk, Sergii V., et al.
Publicado: (2022)

Atomism, Boltzmann and nonequilibrium statistical mechanics
por: Gallavotti, G
Publicado: (1997)

A Finite Element Solution of Lateral Periodic Poisson–Boltzmann Model for Membrane Channel Proteins
por: Ji, Nan, et al.
Publicado: (2018)

Ludwig Boltzmann: The Man Who Trusted Atoms
por: Cercignani, Carlo
Publicado: (1998)

The solution of the Poisson-Boltzmann equation for self-consistent potential of infinite, random, nonlinear and non-uniform system
por: Rasulova, M Yu
Publicado: (1998)

Comparison of Molecular Dynamics with Classical Density Functional and Poisson–Boltzmann Theories of the Electric Double Layer in Nanochannels
por: Lee, Jonathan W., et al.
Publicado: (2012)

A Newton-like iterative method implemented in the DelPhi for solving the nonlinear Poisson-Boltzmann equation
por: Li, Chuan, et al.
Publicado: (2020)

Measurement of Solvation Ability of Solvents by Porphyrin-Based Solvation/Desolvation Indicators
por: Sugimoto, Motonobu, et al.
Publicado: (2020)

Applicability of the linearized Poisson–Boltzmann theory to contact angle problems and application to the carbon dioxide–brine–solid systems
por: Amadu, Mumuni, et al.
Publicado: (2022)

Efficient determination of accurate atomic polarizabilities for polarizeable embedding calculations
por: Schröder, Heiner, et al.
Publicado: (2016)

Boltzmann's atom: the great debate that launched a revolution in physics
por: Lindley, David
Publicado: (2001)

Nuclear radii
por: Schopper, H
Publicado: (1967)

Solvation of Na(+), K(+), and Their Dimers in Helium
por: An der Lan, Lukas, et al.
Publicado: (2012)

Use of the Multilayer Fragment Molecular Orbital Method to Predict the Rank Order of Protein–Ligand Binding Affinities: A Case Study Using Tankyrase 2 Inhibitors
por: Okimoto, Noriaki, et al.
Publicado: (2018)

Molecular Dynamics Study of Conformational Changes of Tankyrase 2 Binding Subsites upon Ligand Binding
por: Hirano, Yoshinori, et al.
Publicado: (2021)

Global properties of atomic nuclei: Masses, radii and modern methods to measure them
por: Kowalska, Magdalena
Publicado: (2016)

Electric Double Layer and Orientational Ordering of Water Dipoles in Narrow Channels within a Modified Langevin Poisson-Boltzmann Model
por: Drab, Mitja, et al.
Publicado: (2020)

Renormalized charge and dielectric effects in colloidal interactions: a numerical solution of the nonlinear Poisson–Boltzmann equation for unknown boundary conditions
por: Schlaich, Alexander, et al.
Publicado: (2023)

MDGRAPE-4: a special-purpose computer system for molecular dynamics simulations
por: Ohmura, Itta, et al.
Publicado: (2014)

The variability of MR axon radii estimates in the human white matter
por: Veraart, Jelle, et al.
Publicado: (2021)

Atoms, mechanics, and probability: Ludwig Boltzmann's statistico-mechanical writings : an exegesis
por: Darrigol, Olivier
Publicado: (2018)

The Influence of Solvent on the Crystal Packing of Ethacridinium Phthalate Solvates
por: Mirocki, Artur, et al.
Publicado: (2020)

Accurate Bond Lengths to Hydrogen Atoms from Single‐Crystal X‐ray Diffraction by Including Estimated Hydrogen ADPs and Comparison to Neutron and QM/MM Benchmarks
por: Dittrich, Birger, et al.
Publicado: (2017)

Potential of mean force between oppositely charged nanoparticles: A comprehensive comparison between Poisson–Boltzmann theory and Monte Carlo simulations
por: Zhang, Jin-Si, et al.
Publicado: (2017)

Nuclear charge radii
por: Schopper, H
Publicado: (2004)

Cannot write session to /tmp/vufind_sessions/sess_6gn7kvqdiqg1or93avbvrvadov