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Development of CHARMM Polarizable Force Field for Nucleic Acid Bases Based on the Classical Drude Oscillator Model
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Outgoing claims: the papers this work cites, builds on, or argues with.
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Atomistic insights into the effects of hydrogen bonds on the melting process and heat conduction of erythritol as a promising latent heat storage material
inferred← citeshttps://doi.org/10.1016/j.jmgm.2013.10.008openalex-snapshot
Investigation of base pairs containing oxidized guanine using ab initio method and ABEEMσπ polarizable force field
inferred← citeshttps://doi.org/10.1016/j.jmgm.2022.108264openalex-snapshot
Exploring the multiple conformational states of RNA genome through interhelical dynamics and network analysis
inferred← citeshttps://doi.org/10.1016/j.ymeth.2012.04.005openalex-snapshot
Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures
inferred← citeshttps://doi.org/10.1016/j.ymeth.2013.05.025openalex-snapshot
How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists
inferred← citeshttps://doi.org/10.1021/acs.chemrev.5b00505openalex-snapshot
An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications
inferred← citeshttps://doi.org/10.1021/acs.chemrev.6b00440openalex-snapshot
Metal Ion Modeling Using Classical Mechanics
inferred← citeshttps://doi.org/10.1021/acs.chemrev.8b00763openalex-snapshot
Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00645openalex-snapshot
Atom Types Independent Molecular Mechanics Method for Predicting the Conformational Energy of Small Molecules
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00132openalex-snapshot
Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator
inferred← citeshttps://doi.org/10.1021/acs.jctc.1c00107openalex-snapshot
Water-Mediated Oxidation of Guanine by a Repair Enzyme: Simulation Using the ABEEM Polarizable Force Field
inferred← citeshttps://doi.org/10.1021/acs.jctc.1c01166openalex-snapshot
Deep Neural Network Model to Predict the Electrostatic Parameters in the Polarizable Classical Drude Oscillator Force Field
inferred← citeshttps://doi.org/10.1021/acs.jctc.3c00203openalex-snapshot
Drude Polarizable Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c00966openalex-snapshot
Revised 4-Point Water Model for the Classical Drude Oscillator Polarizable Force Field: SWM4-HLJ
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c01108openalex-snapshot
Advances and Challenges in Milestoning Simulations for Drug–Target Kinetics
inferred← citeshttps://doi.org/10.1021/acs.jctc.5b00716openalex-snapshot
Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA
inferred← citeshttps://doi.org/10.1021/acs.jctc.5b01115openalex-snapshot
To Polarize or Not to Polarize? Charge-on-Spring versus KBFF Models for Water and Methanol Bulk and Vapor–Liquid Interfacial Mixtures
inferred← citeshttps://doi.org/10.1021/acs.jctc.6b00918openalex-snapshot
Polarizable Multipole-Based Force Field for Aromatic Molecules and Nucleobases
inferred← citeshttps://doi.org/10.1021/acs.jctc.6b01206openalex-snapshot
Development of the ABEEMσπ Polarization Force Field for Base Pairs with Amino Acid Residue Complexes
inferred← citeshttps://doi.org/10.1021/acs.jctc.7b00067openalex-snapshot
Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics
inferred← citeshttps://doi.org/10.1021/acs.jctc.7b00262openalex-snapshot
Drude Polarizable Force Field for Molecular Dynamics Simulations of Saturated and Unsaturated Zwitterionic Lipids
inferred← citeshttps://doi.org/10.1021/acs.jctc.7b00522openalex-snapshot
Evaluating Force-Field London Dispersion Coefficients Using the Exchange-Hole Dipole Moment Model
inferred← citeshttps://doi.org/10.1021/acs.jctc.7b01169openalex-snapshot
AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids
inferred← citeshttps://doi.org/10.1021/acs.jctc.8b00175openalex-snapshot
CHARMM Drude Polarizable Force Field for Glycosidic Linkages Involving Pyranoses and Furanoses
inferred← citeshttps://doi.org/10.1021/acs.jctc.9b00415openalex-snapshot
Toward First-Principles-Level Polarization Energies in Force Fields: A Gaussian Basis for the Atom-Condensed Kohn–Sham Method
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.3c01069openalex-snapshot
Modeling Substrate Entry into the P-Glycoprotein Efflux Pump at the Blood–Brain Barrier
inferred← citeshttps://doi.org/10.1021/acs.jpca.8b04418openalex-snapshot
Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg2+
inferred← citeshttps://doi.org/10.1021/acs.jpcb.1c08340openalex-snapshot
Computational and Experimental Characterization of rDNA and rRNA G-Quadruplexes
inferred← citeshttps://doi.org/10.1021/acs.jpcb.2c04245openalex-snapshot
Extension of the CHARMM Classical Drude Polarizable Force Field to N- and O-Linked Glycopeptides and Glycoproteins
inferred← citeshttps://doi.org/10.1021/acs.jpcb.2c06227openalex-snapshot
Polarizable Molecular Block Model: Toward the Development of an Induced Dipole Force Field for DNA
inferred← citeshttps://doi.org/10.1021/acs.jpcb.3c07356openalex-snapshot
Updates to Protex for Simulating Proton Transfers in an Ionic Liquid
inferred← citeshttps://doi.org/10.1021/acs.jpcb.4c04100openalex-snapshot
CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed
inferred← citeshttps://doi.org/10.1021/acs.jpcb.5b01695openalex-snapshot
Stacked and H-Bonded Cytosine Dimers. Analysis of the Intermolecular Interaction Energies by Parallel Quantum Chemistry and Polarizable Molecular Mechanics.
inferred← citeshttps://doi.org/10.1021/acs.jpcb.5b01767openalex-snapshot
CHARMM Drude Polarizable Force Field for Aldopentofuranoses and Methyl-aldopentofuranosides
inferred← citeshttps://doi.org/10.1021/acs.jpcb.5b09041openalex-snapshot
Polarizable Force Field with a σ-Hole for Liquid and Aqueous Bromomethane
inferred← citeshttps://doi.org/10.1021/acs.jpcb.6b09262openalex-snapshot
Balancing the Interactions of Mg2+ in Aqueous Solution and with Nucleic Acid Moieties For a Polarizable Force Field Based on the Classical Drude Oscillator Model
inferred← citeshttps://doi.org/10.1021/acs.jpcc.5b04805openalex-snapshot
Polarization Effect and Electric Potential Changes in the Stimuli-Responsive Molecular Monolayers Under an External Electric Field
inferred← citeshttps://doi.org/10.1021/acs.jpcc.5b11999openalex-snapshot
Computational Analysis of Sugar Alcohols as Phase-Change Material: Insight into the Molecular Mechanism of Thermal Energy Storage
inferred← citeshttps://doi.org/10.1021/acs.jpclett.4c03451openalex-snapshot
Computationally Efficient Polarizable MD Simulations: A Simple Water Model for the Classical Drude Oscillator Polarizable Force Field
inferred← citeshttps://doi.org/10.1021/acsami.3c12262openalex-snapshot
Unveiling DNA Translocation in Pristine Graphene Nanopores: Understanding Pore Clogging via Polarizable Simulations
inferred← citeshttps://doi.org/10.1021/ar2001217openalex-snapshot
Frontiers in Molecular Dynamics Simulations of DNA
inferred← citeshttps://doi.org/10.1021/ct200723yopenalex-snapshot
Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium
inferred← citeshttps://doi.org/10.1021/ct300722eopenalex-snapshot
Solvent Boundary Potentials for Hybrid QM/MM Computations Using Classical Drude Oscillators: A Fully Polarizable Model
inferred← citeshttps://doi.org/10.1021/ct400116gopenalex-snapshot
Matching of Additive and Polarizable Force Fields for Multiscale Condensed Phase Simulations
inferred← citeshttps://doi.org/10.1021/ct400313nopenalex-snapshot
Automated Optimization of Potential Parameters
inferred← citeshttps://doi.org/10.1021/ct400514popenalex-snapshot
Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units
inferred← citeshttps://doi.org/10.1021/ct400781bopenalex-snapshot
Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator
inferred← citeshttps://doi.org/10.1021/ct500319aopenalex-snapshot
Including the Dispersion Attraction into Structure-Adapted Fast Multipole Expansions for MD Simulations
inferred← citeshttps://doi.org/10.1021/ct500803ropenalex-snapshot
Systematic Improvement of Potential-Derived Atomic Multipoles and Redundancy of the Electrostatic Parameter Space
inferred← citeshttps://doi.org/10.1021/jp211385eopenalex-snapshot
Charge Transfer Effects in the GroEL–GroES Chaperonin Tetramer in Solution
inferred← citeshttps://doi.org/10.1021/jp402860eopenalex-snapshot
A Polarizable Force Field of Dipalmitoylphosphatidylcholine Based on the Classical Drude Model for Molecular Dynamics Simulations of Lipids
inferred← citeshttps://doi.org/10.1021/jp412696mopenalex-snapshot
Polarizable Empirical Force Field for Hexopyranose Monosaccharides Based on the Classical Drude Oscillator
inferred← citeshttps://doi.org/10.1021/jp503469sopenalex-snapshot
Balancing the Interactions of Ions, Water, and DNA in the Drude Polarizable Force Field
inferred← citeshttps://doi.org/10.1021/jp507692hopenalex-snapshot
Conformation Dynamics and Polarization Effect of α,α-Trehalose in a Vacuum and in Aqueous and Salt Solutions
inferred← citeshttps://doi.org/10.1039/9781782626947-00273openalex-snapshot
Concepts and Modeling for Charge Transport in Organic Electronic Materials
inferred← citeshttps://doi.org/10.1039/9781788010139-00039openalex-snapshot
Molecular Dynamics Computer Simulations of Biological Systems
inferred← citeshttps://doi.org/10.1039/9781849735049-00023openalex-snapshot
Towards Biomolecular Simulations with Explicit Inclusion of Polarizability: Development of a CHARMM Polarizable Force Field based on the Classical Drude Oscillator Model
inferred← citeshttps://doi.org/10.1039/c2sm25690hopenalex-snapshot
Insight into nucleic acid counterion interactions from inside molecular dynamics simulations is “worth its salt”
inferred← citeshttps://doi.org/10.1039/c4cp02401jopenalex-snapshot
A comparison between QM/MM and QM/QM based fitting of condensed-phase atomic polarizabilities
inferred← citeshttps://doi.org/10.1039/c5ob00622hopenalex-snapshot
Tetrahydrofuran amino acid-containing gramicidin S analogues with improved biological profiles
inferred← citeshttps://doi.org/10.1039/c6cp02509aopenalex-snapshot
Calculating binding free energies of host–guest systems using the AMOEBA polarizable force field
inferred← citeshttps://doi.org/10.1039/d0nr08796copenalex-snapshot
Polarization influences the evolution of nucleobase–graphene interactions
inferred← citeshttps://doi.org/10.1039/d2cp05873aopenalex-snapshot
Development of a QM/MM(ABEEM) method combined with a polarizable force field to investigate the excision reaction mechanism of damaged thymine
inferred← citeshttps://doi.org/10.1039/d3cp04060gopenalex-snapshot
From bonds to interactions: comprehensive molecular characterization via polarizable bond-dipole approach
inferred← citeshttps://doi.org/10.1039/d6cp00313copenalex-snapshot
Dissecting urea–RNA interactions in SARS-CoV-2 virus: nucleobases as the primary denaturation hotspots
inferred← citeshttps://doi.org/10.1063/1.3700157openalex-snapshot
Multi-layer coarse-graining polarization model for treating electrostatic interactions of solvated α-conotoxin peptides
inferred← citeshttps://doi.org/10.1063/1.4773821openalex-snapshot
How well can polarization models of pairwise nonadditive forces describe liquid water?
inferred← citeshttps://doi.org/10.1063/1.4984113openalex-snapshot
Mapping the Drude polarizable force field onto a multipole and induced dipole model
inferred← citeshttps://doi.org/10.1063/1.5009551openalex-snapshot
Perspective: Ab initio force field methods derived from quantum mechanics
inferred← citeshttps://doi.org/10.1063/5.0278180openalex-snapshot
Performance of the bond capacity model for charge polarization in classical molecular dynamics
inferred← citeshttps://doi.org/10.1080/08927022.2014.913792openalex-snapshot
Progress in molecular modelling of DNA materials
inferred← citeshttps://doi.org/10.1080/08927022.2020.1725003openalex-snapshot
Molecular dynamics free energy simulations of ATP:Mg2+ and ADP:Mg2+ using the polarisable force field AMOEBA
inferred← citeshttps://doi.org/10.1088/1674-1056/abb7f7openalex-snapshot
Effect of interaction between loop bases and ions on stability of G-quadruplex DNA*
inferred← citeshttps://doi.org/10.1093/nar/gkag871openalex-snapshot
Drude SILCS-Nucleic: harnessing explicit electronic polarization in targeting RNA and DNA for drug design
inferred← citeshttps://doi.org/10.1098/rsif.2011.0584openalex-snapshot
Flexibility and binding affinity in protein–ligand, protein–protein and multi-component protein interactions: limitations of current computational approaches
inferred← citeshttps://doi.org/10.1115/1.4045667openalex-snapshot
Contribution of the Hydroxyl Group on Interfacial Heat Conduction of Monohydric Alcohols: A Molecular Dynamics Study
inferred← citeshttps://doi.org/10.1134/s0026893326700019openalex-snapshot
Modern Methods of Molecular Modeling of Aptamers
inferred← citeshttps://doi.org/10.1134/s1811238223700285openalex-snapshot
History and Perspectives of Atomistic Simulation of Polysaccharides
inferred← citeshttps://doi.org/10.1201/b21343-10openalex-snapshot
Explicit Inclusion of Induced Polarization in Atomistic Force Fields Based on the Classical Drude Oscillator Model
inferred← citeshttps://doi.org/10.1201/b21343-9openalex-snapshot
Explicit Inclusion of Induced Polarization in Atomistic Force Fields Based on the Classical Drude Oscillator Model
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1003113openalex-snapshot
Impact of Ribosomal Modification on the Binding of the Antibiotic Telithromycin Using a Combined Grand Canonical Monte Carlo/Molecular Dynamics Simulation Approach
inferred← citeshttps://doi.org/10.31857/s2308114723700231openalex-snapshot
ИСТОРИЯ И ПЕРСПЕКТИВЫ АТОМИСТИЧЕСКОГО МОДЕЛИРОВАНИЯ ПОЛИСАХАРИДОВ
inferred← citeshttps://doi.org/10.3389/fphar.2025.1532697openalex-snapshot
The interplay of polarizable water and protein in the activation of the M2 channel
inferred← citeshttps://doi.org/10.3390/ijms160715872openalex-snapshot
MD Simulations of tRNA and Aminoacyl-tRNA Synthetases: Dynamics, Folding, Binding, and Allostery
inferred← citeshttps://doi.org/10.34297/ajbsr.2021.13.001895openalex-snapshot
Significance of MD Simulation in Pharmaceutical Sciences: A Review
inferred← citeshttps://doi.org/10.4018/978-1-4666-8811-7.ch014openalex-snapshot
Molecular Dynamics Simulations for Biological Systems
inferred← citeshttps://doi.org/10.4018/978-1-5225-1762-7.ch040openalex-snapshot
Molecular Dynamics Simulations for Biological Systems
inferred← citeshttps://doi.org/10.48550/arxiv.1802.10358openalex-snapshot
Charge Transfer in Classical Molecular Dynamics Simulations of Met-enkephalin: Improving Traditional Force Field with Data Driven Models
inferred← citeshttps://doi.org/10.5772/intechopen.74939openalex-snapshot
Modeling Soft Supramolecular Nanostructures by Molecular Simulations
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