Cargando…

Benchmarking the Drude Polarizable Force Field Using the r(GACC) Tetranucleotide

[Image: see text] Polarizable force fields, in particular, the Drude polarizable force field (Drude FF), may hold the key to more accurately modeling biomolecules with molecular dynamics simulations by explicitly accounting for atomic polarizability. Previous work has shown promising results in simu...

Descripción completa

Detalles Bibliográficos
Autores principales:	Winkler, Lauren, Cheatham, Thomas E.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	American Chemical Society 2023
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10131218/ https://www.ncbi.nlm.nih.gov/pubmed/36996447 http://dx.doi.org/10.1021/acs.jcim.3c00250

Ejemplares similares

Representation of Ion–Protein Interactions Using the Drude Polarizable Force-Field
por: Li, Hui, et al.
Publicado: (2015)

Balancing the Interactions of Ions, Water, and DNA in the Drude Polarizable Force Field
por: Savelyev, Alexey, et al.
Publicado: (2014)

Polarizable Empirical Force Field for Hexopyranose Monosaccharides Based on the Classical Drude Oscillator
por: Patel, Dhilon S., et al.
Publicado: (2014)

Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model
por: Huang, Jing, et al.
Publicado: (2014)

Benchmarking AMBER Force Fields for RNA: Comparisons to NMR Spectra for Single-Stranded r(GACC) Are Improved by Revised χ Torsions
por: Yildirim, Ilyas, et al.
Publicado: (2011)

An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications
por: Lemkul, Justin A., et al.
Publicado: (2016)

Binding Energy and Free Energy of Calcium Ion to Calmodulin EF-Hands with the Drude Polarizable Force Field
por: Tan, Qiaozhu, et al.
Publicado: (2021)

Interfacing the Core-Shell or the Drude Polarizable Force Field With Car–Parrinello Molecular Dynamics for QM/MM Simulations
por: Sahoo, Sudhir K., et al.
Publicado: (2018)

Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields
por: Bergonzo, Christina, et al.
Publicado: (2015)

Glycosidic α-linked mannopyranose disaccharides: an NMR spectroscopy and molecular dynamics simulation study employing additive and Drude polarizable force fields
por: Ruda, Alessandro, et al.
Publicado: (2022)

Parameterization to NDDO-based polarizable force field
por: Thomas, Heike, et al.
Publicado: (2014)

RNA-protein complexes and force field polarizability
por: Baltrukevich, Hanna, et al.
Publicado: (2023)

Exploring optimization strategies for improving explicit water models: Rigid n-point model and polarizable model based on Drude oscillator
por: Xiong, Yeyue, et al.
Publicado: (2019)

Evaluation of Representations and Response Models for Polarizable Force Fields
por: Li, Amanda, et al.
Publicado: (2016)

Anti-drude metal of bosons
por: Masella, Guido, et al.
Publicado: (2022)

Polarizable Water Model for the Coarse-Grained MARTINI Force Field
por: Yesylevskyy, Semen O., et al.
Publicado: (2010)

Polarizable Multipole-Based Force Field for Dimethyl and Trimethyl Phosphate
por: Zhang, Changsheng, et al.
Publicado: (2015)

Polarizable Multipole-Based Force Field for Aromatic Molecules and Nucleobases
por: Zhang, Changsheng, et al.
Publicado: (2016)

Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields
por: Bedrov, Dmitry, et al.
Publicado: (2019)

Fractional Derivative Modification of Drude Model
por: Karpiński, Karol, et al.
Publicado: (2021)

POSSIM: Parameterizing Complete Second-Order Polarizable Force Field for Proteins
por: Li, Xinbi, et al.
Publicado: (2014)

Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide
por: Bergonzo, Christina, et al.
Publicado: (2013)

Structures and Dynamics of DNA Mini-Dumbbells Are Force Field Dependent
por: Winkler, Lauren, et al.
Publicado: (2023)

Realistic sampling of amino acid geometries for a multipolar polarizable force field
por: Hughes, Timothy J., et al.
Publicado: (2015)

Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field
por: Mohamed, Noor Asidah, et al.
Publicado: (2016)

Self-Consistent Parameterization of DNA Residues for the Non-Polarizable AMBER Force Fields
por: Schneider, Amelia L., et al.
Publicado: (2022)

Static Polarizabilities at the Basis Set Limit: A Benchmark of 124 Species
por: Brakestad, Anders, et al.
Publicado: (2020)

Modeling Organochlorine Compounds and the σ-Hole Effect Using a Polarizable Multipole Force Field
por: Mu, Xiaojiao, et al.
Publicado: (2014)

Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units
por: Lindert, Steffen, et al.
Publicado: (2013)

Hydration Free Energy from Orthogonal Space Random Walk and Polarizable Force Field
por: Abella, Jayvee R., et al.
Publicado: (2014)

Computational Study of PCSK9-EGFA Complex with Effective Polarizable Bond Force Field
por: Chen, Jian, et al.
Publicado: (2018)

Polarizable Force Fields for CO(2) and CH(4) Adsorption in M-MOF-74
por: Becker, Tim M., et al.
Publicado: (2017)

Deriving a Polarizable Force Field for Biomolecular Building Blocks with Minimal Empirical Calibration
por: Visscher, Koen M., et al.
Publicado: (2020)

Current Status of AMOEBA–IL: A Multipolar/Polarizable Force Field for Ionic Liquids
por: Vázquez-Montelongo, Erik Antonio, et al.
Publicado: (2020)

Capturing charge and size effects of ions at the graphene–electrolyte interface using polarizable force field simulations
por: H., Hemanth, et al.
Publicado: (2023)

Computational study on the binding of Mango-II RNA aptamer and fluorogen using the polarizable force field AMOEBA
por: Yang, Xudong, et al.
Publicado: (2022)

A Polarizable Atomic Multipole-Based Force Field for Molecular Dynamics Simulations of Anionic Lipids
por: Chu, Huiying, et al.
Publicado: (2017)

Polarizable Force Field for CO(2) in M-MOF-74 Derived from Quantum Mechanics
por: Becker, Tim M., et al.
Publicado: (2018)

Tetranucleotide usage highlights genomic heterogeneity among mycobacteriophages
por: Siranosian, Benjamin, et al.
Publicado: (2015)

Deriving Force-Field Parameters from First Principles Using a Polarizable and Higher Order Dispersion Model
por: Visscher, Koen M., et al.
Publicado: (2019)

Cannot write session to /tmp/vufind_sessions/sess_efgt0vrt7q4vl80hr20vhbkmu1