QM/MM Free-Energy Perturbation Compared to Thermodynamic Integration and Umbrella Sampling: Application to an Enzymatic Reaction
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Correlating protein hot spot surface analysis using ProBiS with simulated free energies of protein-protein interfacial residuesIdentification of a second GTP-bound magnesium ion in archaeal initiation factor 2.Predicting binding affinities of host-guest systems in the SAMPL3 blind challenge: the performance of relative free energy calculationsThe origin of the cooperativity in the streptavidin-biotin system: A computational investigation through molecular dynamics simulations.Energy Landscape Topography Reveals the Underlying Link Between Binding Specificity and Activity of EnzymesFree energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methodsDevelopment and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes.Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method.A pseudobond parametrization for improved electrostatics in quantum mechanical/molecular mechanical simulations of enzymes.Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level.Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting SchemesTheoretical prediction of drug-receptor interactions.On the accuracy of one- and two-particle solvation entropies.Reductive half-reaction of aldehyde oxidoreductase toward acetaldehyde: Ab initio and free energy quantum mechanical/molecular mechanical calculations.Communication: Constructing an implicit quantum mechanical/molecular mechanics solvent model by coarse-graining explicit solvent.Toward accurate barriers for enzymatic reactions: QM/MM case study on p-hydroxybenzoate hydroxylase.Quantum Chemical Analyses of BH4- and BH3 OH- Hydride Transfers to CO2 in Aqueous Solution with Potentials of Mean Force.Superlinearly converging dimer method for transition state search.Umbrella integration with higher-order correction terms.Reduction potentials and acidity constants of Mn superoxide dismutase calculated by QM/MM free-energy methods.Non-Boltzmann sampling and Bennett's acceptance ratio method: how to profit from bending the rules.Automated Exploration of Free Energy Landscapes Based on Umbrella Integration.Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface.Cyclization Reaction Catalyzed by Cyclodipeptide Synthases Relies on a Conserved Tyrosine Residue.Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challengeMethodological aspects of QM/MM calculations: A case study on matrix metalloproteinase-2Quantum mechanics/molecular mechanics dual Hamiltonian free energy perturbationFinite-temperature effects in enzymatic reactions — Insights from QM/MM free-energy simulationsAnalysis of the statistical error in umbrella sampling simulations by umbrella integrationConvergence of single-step free energy perturbationEnhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-AccelerationQM/MM-Methoden für biomolekulare SystemeNovel Molecular-Dynamics-Based Protocols for Phase Space Sampling in Complex Systems
P2860
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P2860
QM/MM Free-Energy Perturbation Compared to Thermodynamic Integration and Umbrella Sampling: Application to an Enzymatic Reaction
description
2006 nî lūn-bûn
@nan
2006 թուականի Մարտին հրատարակուած գիտական յօդուած
@hyw
2006 թվականի մարտին հրատարակված գիտական հոդված
@hy
2006年の論文
@ja
2006年論文
@yue
2006年論文
@zh-hant
2006年論文
@zh-hk
2006年論文
@zh-mo
2006年論文
@zh-tw
2006年论文
@wuu
name
QM/MM Free-Energy Perturbation ...... ation to an Enzymatic Reaction
@ast
QM/MM Free-Energy Perturbation ...... ation to an Enzymatic Reaction
@en
type
label
QM/MM Free-Energy Perturbation ...... ation to an Enzymatic Reaction
@ast
QM/MM Free-Energy Perturbation ...... ation to an Enzymatic Reaction
@en
prefLabel
QM/MM Free-Energy Perturbation ...... ation to an Enzymatic Reaction
@ast
QM/MM Free-Energy Perturbation ...... ation to an Enzymatic Reaction
@en
P50
P3181
P356
P1476
QM/MM Free-Energy Perturbation ...... ation to an Enzymatic Reaction
@en
P2093
Nikolaj Otte
Stephan Thiel
P304
P3181
P356
10.1021/CT050252W
P577
2006-03-01T00:00:00Z