Assessing the efficiency of free energy calculation methods.
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Insertion of short amino-functionalized single-walled carbon nanotubes into phospholipid bilayer occurs by passive diffusionGating of a pH-sensitive K(2P) potassium channel by an electrostatic effect of basic sensor residues on the selectivity filterBuilding a foundation for structure-based cellulosome design for cellulosic ethanol: Insight into cohesin-dockerin complexation from computer simulationSecondary and tertiary structure elasticity of titin Z1Z2 and a titin chain model.Analysis of the selectivity filter of the voltage-gated sodium channel Na(v)RhFree energetics of rigid body association of ubiquitin binding domains: a biochemical model for binding mediated by hydrophobic interaction.Conformational dynamics and ligand binding in the multi-domain protein PDC109Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor.Tertiary and secondary structure elasticity of a six-Ig titin chain.Comparison of mode analyses at different resolutions applied to nucleic acid systems.Back to the future: can physical models of passive membrane permeability help reduce drug candidate attrition and move us beyond QSPR?Free energetics of arginine permeation into model DMPC lipid bilayers: coupling of effective counterion concentration and lateral bilayer dimensionsArginine in membranes: the connection between molecular dynamics simulations and translocon-mediated insertion experimentsHow does (E)-2-(acetamidomethylene)succinate bind to its hydrolase? From the binding process to the final result.Molecular dynamics simulation of the antiamoebin ion channel: linking structure and conductance.An AIMD study of the CPD repair mechanism in water: reaction free energy surface and mechanistic implications.The adaptive biasing force method: everything you always wanted to know but were afraid to askMolecular restraints in the permeation pathway of ion channels.Oligomerization state of photosynthetic core complexes is correlated with the dimerization affinity of a transmembrane helixInfluence of Chirality of Crizotinib on Its MTH1 Protein Inhibitory Activity: Insight from Molecular Dynamics Simulations and Binding Free Energy Calculations.Sequence-specific recognition of cancer drug-DNA adducts by HMGB1a repair proteinStepwise substrate translocation mechanism revealed by free energy calculations of doxorubicin in the multidrug transporter AcrB.The effect of sterols on amphotericin B self-aggregation in a lipid bilayer as revealed by free energy simulations.Free energy profile of H-ras membrane anchor upon membrane insertion.The mechanism of Na⁺/K⁺ selectivity in mammalian voltage-gated sodium channels based on molecular dynamics simulationEfficient determination of protein-protein standard binding free energies from first principles.Computational Equilibrium Thermodynamic and Kinetic Analysis of K-Ras Dimerization through an Effector Binding Surface Suggests Limited Functional Role.Impairment on the lateral mobility induced by structural changes underlies the functional deficiency of the lupus-associated polymorphism FcγRIIB-T232.Exploring the pH-dependent substrate transport mechanism of FocA using molecular dynamics simulation.Simulation-Based Approaches for Determining Membrane Permeability of Small CompoundsPeptide backbone sampling convergence with the adaptive biasing force algorithmRigidity and flexibility in the tetrasaccharide linker of proteoglycans from atomic-resolution molecular simulation.Similar membrane affinity of mono- and Di-S-acylated ras membrane anchors: a new twist in the role of protein lipidation.Through the channel and around the channel: Validating and comparing microscopic approaches for the evaluation of free energy profiles for ion penetration through ion channels.Formation of salt bridges mediates internal dimerization of myosin VI medial tail domain.Prediction of 1-octanol-water and air-water partition coefficients for nitro-aromatic compounds from molecular dynamics simulations.Free energy for the permeation of Na(+) and Cl(-) ions and their ion-pair through a zwitterionic dimyristoyl phosphatidylcholine lipid bilayer by umbrella integration with harmonic fourier beads.Enhanced sampling of molecular dynamics simulation of peptides and proteins by double coupling to thermal bath.Overcoming free energy barriers using unconstrained molecular dynamics simulations.On-the-fly reconstruction of free-energy profiles using logarithmic mean-force dynamics.
P2860
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P2860
Assessing the efficiency of free energy calculation methods.
description
2004 nî lūn-bûn
@nan
2004年の論文
@ja
2004年学术文章
@wuu
2004年学术文章
@zh-cn
2004年学术文章
@zh-hans
2004年学术文章
@zh-my
2004年学术文章
@zh-sg
2004年學術文章
@yue
2004年學術文章
@zh
2004年學術文章
@zh-hant
name
Assessing the efficiency of free energy calculation methods.
@en
Assessing the efficiency of free energy calculation methods.
@nl
type
label
Assessing the efficiency of free energy calculation methods.
@en
Assessing the efficiency of free energy calculation methods.
@nl
prefLabel
Assessing the efficiency of free energy calculation methods.
@en
Assessing the efficiency of free energy calculation methods.
@nl
P2093
P2860
P356
P1476
Assessing the efficiency of free energy calculation methods.
@en
P2093
Andrew Pohorille
David Rodriguez-Gomez
Eric Darve
P2860
P304
P356
10.1063/1.1642607
P407
P577
2004-02-01T00:00:00Z