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Testing of the GROMOS Force-Field Parameter Set 54A8: Structural Properties of Electrolyte Solutions, Lipid Bilayers, and Proteins
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Polarizable Simulations with Second-Order Interaction Model—Force Field and Software for Fast Polarizable Calculations: Parameters for Small Model Systems and Free Energy Calculations
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Free energies of ligand binding for structurally diverse compounds
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Polarizable Multipole-Based Force Field for Aromatic Molecules and Nucleobases
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A simple polarizable model of water based on classical Drude oscillators
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Induced Dipole–Dipole Interactions Influence the Unfolding Pathways of Wild-Type and Mutant Amyloid β-Peptides
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Solvent interactions determine carbohydrate conformation
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Editorial overview: Recent applications of x-ray and neutron scattering techniques in colloid and interfacial science, characterised by increasing diversity and complexity
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Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field
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Comparison of simple potential functions for simulating liquid water
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July 1983 |
Binding structures of tri-N-acetyl-β-glucosamine in hen egg white lysozyme using molecular dynamics with a polarizable force field
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GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
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Understanding the Dielectric Properties of Liquid Amides from a Polarizable Force Field
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Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Methods in Computational Enzymology
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CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model
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LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands
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Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields
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Constant pressure molecular dynamics simulation: The Langevin piston method
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CHARMM: The biomolecular simulation program
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Validation of the 53A6 GROMOS force field
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Zif268 protein–DNA complex refined at 1.6å: a model system for understanding zinc finger–DNA interactions
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Molecular Simulations of Gram-Negative Bacterial Membranes Come of Age
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A Polarizable Force Field of Dipalmitoylphosphatidylcholine Based on the Classical Drude Model for Molecular Dynamics Simulations of Lipids
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Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field
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Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model
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Conformation of the TAR RNA-arginine complex by NMR spectroscopy
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FRET in membrane biophysics: an overview
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Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units
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Structure of ubiquitin refined at 1.8 Å resolution
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CHARMM-GUI supports the Amber force fields
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CHARMM-GUI Polymer Builder for Modeling and Simulation of Synthetic Polymers
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Mechanism of Hyaluronan Degradation byStreptococcus pneumoniae Hyaluronate Lyase
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Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins
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Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ 1 and χ 2 Dihedral Angles
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New spherical-cutoff methods for long-range forces in macromolecular simulation
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CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field
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Balancing the Interactions of Mg 2+ in Aqueous Solution and with Nucleic Acid Moieties For a Polarizable Force Field Based on the Classical Drude Oscillator Model
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October 2016 |
CHARMM Drude Polarizable Force Field for Glycosidic Linkages Involving Pyranoses and Furanoses
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April 2018 |
Drude Polarizable Force Field Parametrization of Carboxylate and N-Acetyl Amine Carbohydrate Derivatives
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August 2019 |
Same fold, different properties: polarizable molecular dynamics simulations of telomeric and TERRA G-quadruplexes
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Strong scaling of general-purpose molecular dynamics simulations on GPUs
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July 2015 |
Proper balance of solvent-solute and solute-solute interactions in the treatment of the diffusion of glucose using the Drude polarizable force field
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March 2018 |
Single-Molecule Experiments in Vitro and in Silico
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May 2007 |
Exploring Ion Permeation Energetics in Gramicidin A Using Polarizable Charge Equilibration Force Fields
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CHARMM All-Atom Additive Force Field for Sphingomyelin: Elucidation of Hydrogen Bonding and of Positive Curvature
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July 2014 |
Implementation of accelerated molecular dynamics in NAMD
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CHARMM Additive All-Atom Force Field for Carbohydrate Derivatives and Its Utility in Polysaccharide and Carbohydrate–Protein Modeling
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August 2011 |
Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics
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January 2017 |
Machine learning for molecular and materials science
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July 2018 |
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
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CHARMM-GUI PDB Manipulator for Advanced Modeling and Simulations of Proteins Containing Nonstandard Residues
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August 2014 |
Molecular Simulation and Biochemical Studies Support an Elevator-type Transport Mechanism in EIIC
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June 2017 |
Polarizable Atomic Multipole-Based Molecular Mechanics for Organic Molecules
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August 2011 |
Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA
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April 2011 |
Cryo-EM in drug discovery: achievements, limitations and prospects
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June 2018 |
GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations: GENESIS
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Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 5, Issue 4
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May 2015 |
Polarization effects in molecular mechanical force fields
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July 2009 |
Efficient Simulation Method for Polarizable Protein Force Fields: Application to the Simulation of BPTI in Liquid Water
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December 2004 |
Charge Transfer Models of Zinc and Magnesium in Water
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March 2015 |
Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks
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May 2018 |
Preferred conformations of lipooligosaccharides and oligosaccharides of Moraxella catarrhalis
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October 2019 |
CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates
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February 2019 |
Glycan fragment database: a database of PDB-based glycan 3D structures
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October 2012 |
Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium
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December 2011 |
Thermalized Drude Oscillators with the LAMMPS Molecular Dynamics Simulator
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December 2015 |
The Amber biomolecular simulation programs
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January 2005 |
Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model
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July 2016 |
Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field
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June 2015 |
Carbohydrate force fields: Carbohydrate force fields
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Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 2, Issue 4
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P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation
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Toward Prediction of Electrostatic Parameters for Force Fields That Explicitly Treat Electronic Polarization
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OPM database and PPM web server: resources for positioning of proteins in membranes
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CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields
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Glycan reader: Automated sugar identification and simulation preparation for carbohydrates and glycoproteins
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August 2011 |
Polarizable Empirical Force Field for Hexopyranose Monosaccharides Based on the Classical Drude Oscillator
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An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications
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Solvent-Induced Forces between Two Hydrophilic Groups
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A unified formulation of the constant temperature molecular dynamics methods
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Six-site polarizable model of water based on the classical Drude oscillator
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Structural basis of hyaluronan degradation by Streptococcus pneumoniae hyaluronate lyase
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Parmbsc1: a refined force field for DNA simulations
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Escherichia coli O176 LPS structure and dynamics: A NMR spectroscopy and MD simulation study
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Polarizable Empirical Force Field for Halogen-Containing Compounds Based on the Classical Drude Oscillator
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High-Performance Scalable Molecular Dynamics Simulations of a Polarizable Force Field Based on Classical Drude Oscillators in NAMD
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The Structure of a Sugar Transporter of the Glucose EIIC Superfamily Provides Insight into the Elevator Mechanism of Membrane Transport
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All-atom polarizable force field for DNA based on the classical drude oscillator model
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A polarizable, charge transfer model of water using the drude oscillator: Influence of Charge Transfer on the Drude Oscillator
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Cryo-EM structures reveal coordinated domain motions that govern DNA cleavage by Cas9
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Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field
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CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
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An improved nucleic acid parameter set for the GROMOS force field: Improved Nucleic Acid Parameter Set
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Simulations of disordered proteins and systems with conformational heterogeneity
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Polarizable Empirical Force Field for Acyclic Polyalcohols Based on the Classical Drude Oscillator: Polarizable Force Field for Acyclic Polyols
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Force field development and simulations of intrinsically disordered proteins
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Glycan Reader is improved to recognize most sugar types and chemical modifications in the Protein Data Bank
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Crystal structure of a phosphorylation-coupled saccharide transporter
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Structure of an EIIC sugar transporter trapped in an inward-facing conformation
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Development of a Nonlinear Classical Polarization Model for Liquid Water and Aqueous Solutions: COS/D †
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HIV-1 Tat interactions with cellular 7SK and viral TAR RNAs identifies dual structural mimicry
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Recent developments and applications of the CHARMM force fields
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Balancing the Interactions of Ions, Water, and DNA in the Drude Polarizable Force Field
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Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator
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A smooth particle mesh Ewald method
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CHARMM-GUI 10 years for biomolecular modeling and simulation: Biomolecular Modeling and Simulation
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ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins
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Comparison of Additive and Polarizable Models with Explicit Treatment of Long-Range Lennard-Jones Interactions Using Alkane Simulations
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Constant pressure molecular dynamics algorithms
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Human immunodeficiency virus 1 tat protein binds trans-activation-responsive region (TAR) RNA in vitro.
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A polarizable model of water for molecular dynamics simulations of biomolecules
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A complete view of the genetic diversity of the Escherichia coli O-antigen biosynthesis gene cluster
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