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Adaptive biasing force method for scalar and vector free energy calculations.

Adaptive biasing force method for scalar and vector free energy calculations.

http://www.wikidata.org/entity/Q46830946

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Insights into Protein-Ligand Interactions: Mechanisms, Models, and Methods Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation Pathways and Barriers for Ion Translocation through the 5-HT3A Receptor Channel Exploring volatile general anesthetic binding to a closed membrane-bound bacterial voltage-gated sodium channel via computation Insertion of short amino-functionalized single-walled carbon nanotubes into phospholipid bilayer occurs by passive diffusion A Self-Limiting Electro-Ablation Technique for the Top-Down Synthesis of Large-Area Monolayer Flakes of 2D Materials.Investigation of allosteric modulation mechanism of metabotropic glutamate receptor 1 by molecular dynamics simulations, free energy and weak interaction analysis Search for β2 adrenergic receptor ligands by virtual screening via grid computing and investigation of binding modes by docking and molecular dynamics simulations FtsZ Protofilaments Use a Hinge-Opening Mechanism for Constrictive Force Generation P-loop conformation governed crizotinib resistance in G2032R-mutated ROS1 tyrosine kinase: clues from free energy landscape Breaking the hydrophobicity of the MscL pore: insights into a charge-induced gating mechanism Analysis of the selectivity filter of the voltage-gated sodium channel Na(v)Rh Free energetics of rigid body association of ubiquitin binding domains: a biochemical model for binding mediated by hydrophobic interaction.Revealing inhibition difference between PFI-2 enantiomers against SETD7 by molecular dynamics simulations, binding free energy calculations and unbinding pathway analysis.Smoothed Biasing Forces Yield Unbiased Free Energies with the Extended-System Adaptive Biasing Force Method.Ribonucleotide Reductase Requires Subunit Switching in Hypoxia to Maintain DNA Replication Understanding ligand-receptor non-covalent binding kinetics using molecular modeling.Kinetics of O2 Entry and Exit in Monomeric Sarcosine Oxidase via Markovian Milestoning Molecular Dynamics.Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation.Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics Terminal sialic acids on CD44 N-glycans can block hyaluronan binding by forming competing intramolecular contacts with arginine sidechains.Free energetics of arginine permeation into model DMPC lipid bilayers: coupling of effective counterion concentration and lateral bilayer dimensions The effect of a G:T mispair on the dynamics of DNA Molecular dynamics and brownian dynamics investigation of ion permeation and anesthetic halothane effects on a proton-gated ion channel Molecular dynamics simulation of the antiamoebin ion channel: linking structure and conductance.The adaptive biasing force method: everything you always wanted to know but were afraid to ask Implementation of Accelerated Molecular Dynamics in NAMD Modeling and enhanced sampling of molecular systems with smooth and nonlinear data-driven collective variables.Revealing the favorable dissociation pathway of type II kinase inhibitors via enhanced sampling simulations and two-end-state calculations.Locating landmarks on high-dimensional free energy surfaces.Force-momentum-based self-guided Langevin dynamics: a rapid sampling method that approaches the canonical ensemble.Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition.Molecular dynamics investigation of Cl- and water transport through a eukaryotic CLC transporter.Influence of Chirality of Crizotinib on Its MTH1 Protein Inhibitory Activity: Insight from Molecular Dynamics Simulations and Binding Free Energy Calculations.Single-molecule determination of the face-specific adsorption of Amelogenin's C-terminus on hydroxyapatite.Adsorption mechanism and collapse propensities of the full-length, monomeric Aβ(1-42) on the surface of a single-walled carbon nanotube: a molecular dynamics simulation study.Nucleotide-dependent mechanism of Get3 as elucidated from free energy calculations.Hinge-bending motions in the pore domain of a bacterial voltage-gated sodium channel Protonation of Glu(135) Facilitates the Outward-to-Inward Structural Transition of Fucose Transporter Stepwise substrate translocation mechanism revealed by free energy calculations of doxorubicin in the multidrug transporter AcrB.

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P2860

Adaptive biasing force method for scalar and vector free energy calculations.

http://www.wikidata.org/entity/Q46830946

description

2008 nî lūn-bûn

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2008年の論文

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2008年学术文章

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2008年学术文章

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2008年学术文章

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2008年学术文章

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2008年学术文章

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2008年学术文章

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2008年學術文章

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2008年學術文章

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name

Adaptive biasing force method for scalar and vector free energy calculations.

@en

Adaptive biasing force method for scalar and vector free energy calculations.

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type

label

Adaptive biasing force method for scalar and vector free energy calculations.

@en

Adaptive biasing force method for scalar and vector free energy calculations.

@nl

prefLabel

Adaptive biasing force method for scalar and vector free energy calculations.

@en

Adaptive biasing force method for scalar and vector free energy calculations.

@nl

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Journal of Chemical Physics

P1476

Adaptive biasing force method for scalar and vector free energy calculations.

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P2093

Andrew Pohorille

http://www.w3.org/2001/XMLSchema#string

David Rodríguez-Gómez

http://www.w3.org/2001/XMLSchema#string

Eric Darve

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P2860

Multicanonical ensemble: A new approach to simulate first-order phase transitions

Canonical dynamics: Equilibrium phase-space distributions

Comparison of simple potential functions for simulating liquid water

Determining the density of states for classical statistical models: A random walk algorithm to produce a flat histogram

Efficient, Multiple-Range Random Walk Algorithm to Calculate the Density of States

Scalable molecular dynamics with NAMD

Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations

Secondary and tertiary structure elasticity of titin Z1Z2 and a titin chain model.

Escaping free-energy minima.

Blue moon sampling, vectorial reaction coordinates, and unbiased constrained dynamics.

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144120

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scholarly article

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10.1063/1.2829861

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14

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128

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2008-04-01T00:00:00Z

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5441129

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18412436

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