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Assessing the Current State of Amber Force Field Modifications for DNAProtein-Ligand Electrostatic Binding Free Energies from Explicit and Implicit SolvationMetal Ion Modeling Using Classical MechanicsExploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations.Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulationsUnited polarizable multipole water model for molecular mechanics simulationBinding enthalpy calculations for a neutral host-guest pair yield widely divergent salt effects across water models.Structural study of the Fox-1 RRM protein hydration reveals a role for key water molecules in RRM-RNA recognition.Spatial Decomposition of Translational Water-Water Correlation Entropy in Binding Pockets.Evaluating Force Field Performance in Thermodynamic Calculations of Cyclodextrin Host-Guest Binding: Water Models, Partial Charges, and Host Force Field Parameters.Overview of the SAMPL5 host-guest challenge: Are we doing better?How to understand atomistic molecular dynamics simulations of RNA and protein-RNA complexes?Spermine Condenses DNA, but Not RNA Duplexes.The SAMPL5 host-guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method.Free energy analysis and mechanism of base pair stacking in nicked DNA.GROMOS polarizable charge-on-spring models for liquid urea: COS/U and COS/U2.Accuracy limit of rigid 3-point water models.Implicit Solvent Model for Million-Atom Atomistic Simulations: Insights into the Organization of 30-nm Chromatin Fiber.Accuracy comparison of several common implicit solvent models and their implementations in the context of protein-ligand binding.Insilico direct folding of thrombin-binding aptamer G-quadruplex at all-atom level.Understanding the interactions between sebum triglycerides and water: a molecular dynamics simulation study.RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Non-conformal coarse-grained potentials for water.Physics-based all-atom modeling of RNA energetics and structure.RNA force field with accuracy comparable to state-of-the-art protein force fields.A putative RNA binding protein from Plasmodium vivax apicoplast.The mechanism of the dielectric relaxation in water.New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions.Efficient minimization of multipole electrostatic potentials in torsion space.Unveiling the peculiar hydrogen bonding behavior of solvated N-heterocyclic carbenes.Sequential electron transfer governs the UV-induced self-repair of DNA photolesions.Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations.Structure of HIV TAR in complex with a Lab-Evolved RRM provides insight into duplex RNA recognition and synthesis of a constrained peptide that impairs transcriptionSimulations of lipid bilayers using the CHARMM36 force field with the TIP3P-FB and TIP4P-FB water modelsStructural dynamics of propeller loop: towards folding of RNA G-quadruplexRotational Dynamics of Proteins from Spin Relaxation Times and Molecular Dynamics Simulations
P2860
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P2860
description
2014 nî lūn-bûn
@nan
2014年の論文
@ja
2014年論文
@yue
2014年論文
@zh-hant
2014年論文
@zh-hk
2014年論文
@zh-mo
2014年論文
@zh-tw
2014年论文
@wuu
2014年论文
@zh
2014年论文
@zh-cn
name
Building Water Models: A Different Approach
@en
Building Water Models: A Different Approach
@nl
type
label
Building Water Models: A Different Approach
@en
Building Water Models: A Different Approach
@nl
prefLabel
Building Water Models: A Different Approach
@en
Building Water Models: A Different Approach
@nl
P2860
P356
P1476
Building Water Models: A Different Approach
@en
P2093
Alexey V Onufriev
Saeed Izadi
P2860
P304
P356
10.1021/JZ501780A
P577
2014-10-16T00:00:00Z