Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration (Q57943282)

April 2022 Public Data File from Crossref

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Conformational Sampling of Maltose-transporter Components in Cartesian Collective Variables is Governed by the Low-frequency Normal Modes

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Probing pH-dependent dissociation of HdeA dimers

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Molecular simulation study of cooperativity in hydrophobic association

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Calculation of absolute protein-ligand binding affinity using path and endpoint approaches

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Use of Umbrella Sampling to Calculate the Entrance/Exit Pathway for Z-Pro-Prolinal Inhibitor in Prolyl Oligopeptidase.

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How maltose influences structural changes to bind to maltose-binding protein: results from umbrella sampling simulation

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Computer simulation of the distribution of hexane in a lipid bilayer: spatially resolved free energy, entropy, and enthalpy profiles

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Characterization of interactions between PilA from Pseudomonas aeruginosa strain K and a model membrane

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Convergence of Free Energy Profile of Coumarin in Lipid Bilayer

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Diffusion of 1,2-Dimethoxyethane and 1,2-Dimethoxypropane through Phosphatidycholine Bilayers: A Molecular Dynamics Study

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Conformational changes of β-carotene and zeaxanthin immersed in a model membrane through atomistic molecular dynamics simulations.

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How warfarin's structural diversity influences its phospholipid bilayer membrane permeation.

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Quantum mechanical/molecular mechanical free energy simulations of the glutathione S-transferase (M1-1) reaction with phenanthrene 9,10-oxide

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QM/MM Free-Energy Perturbation Compared to Thermodynamic Integration and Umbrella Sampling: Application to an Enzymatic Reaction

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Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis: the case of histone lysine methyltransferase SET7/9.

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Ab initio QM/MM free-energy studies of arginine deiminase catalysis: the protonation state of the Cys nucleophile

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Revelation of a catalytic calcium-binding site elucidates unusual metal dependence of a human apyrase

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Preferred WMSA catalytic mechanism of the nucleotidyl transfer reaction in human DNA polymerase κ elucidates error-free bypass of a bulky DNA lesion

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Selectivity and permeation of alkali metal ions in K+-channels

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Mechanism of action of cyclophilin a explored by metadynamics simulations

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All-atom models of the membrane-spanning domain of HIV-1 gp41 from metadynamics

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Effect of urea on the β-hairpin conformational ensemble and protein denaturation mechanism.

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Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics

21 January 2018

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Multidimensional view of amyloid fibril nucleation in atomistic detail.

21 January 2018

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Flexible docking in solution using metadynamics

21 January 2018

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Locating binding poses in protein-ligand systems using reconnaissance metadynamics

21 January 2018

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Funnel metadynamics as accurate binding free-energy method

21 January 2018

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Effects of oncogenic mutations on the conformational free-energy landscape of EGFR kinase

21 January 2018

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Crystal structure transformations in SiO2 from classical and ab initio metadynamics.

21 January 2018

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Accurate Rates of the Complex Mechanisms for Growth and Dissolution of Minerals Using a Combination of Rare-Event Theories

21 January 2018

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Water at hydrophobic interfaces delays proton surface-to-bulk transfer and provides a pathway for lateral proton diffusion

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21 January 2018

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21 January 2018

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21 January 2018

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A self-learning algorithm for biased molecular dynamics

21 January 2018

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Probability Distributions for Complex Systems: Adaptive Umbrella Sampling of the Potential Energy

21 January 2018

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Reconstructing the density of states by history-dependent metadynamics.

21 January 2018

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RNA/Peptide Binding Driven by Electrostatics-Insight from Bidirectional Pulling Simulations

21 January 2018

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Quantifying density fluctuations in volumes of all shapes and sizes using indirect umbrella sampling

21 January 2018

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Transition path from two apposed membranes to a stalk obtained by a combination of particle simulations and string method.

21 January 2018

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A Collective Variable for the Efficient Exploration of Protein Beta-Sheet Structures: Application to SH3 and GB1.

21 January 2018

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From A to B in free energy space.

21 January 2018

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Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap.

21 January 2018

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Optimization by Simulated Annealing

21 January 2018

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Choosing weights for simulated tempering

21 January 2018

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Replica-exchange molecular dynamics method for protein folding

21 January 2018

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Speed-up of Monte Carlo simulations by sampling of rejected states

21 January 2018

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Virtual-Move Parallel Tempering

21 January 2018

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Asynchronous replica exchange for molecular simulations

21 January 2018

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Thermostat artifacts in replica exchange molecular dynamics simulations

21 January 2018

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Exchange Often and Properly in Replica Exchange Molecular Dynamics

21 January 2018

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Predicting the signaling state of photoactive yellow protein

21 January 2018

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Initial binding of ions to the interhelical loops of divalent ion transporter CorA: replica exchange molecular dynamics simulation study

21 January 2018

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Trp-cage: Folding free energy landscape in explicit water

21 January 2018

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Folding a protein in a computer: An atomic description of the folding/unfolding of protein A

21 January 2018

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An Implicit Membrane Generalized Born Theory for the Study of Structure, Stability, and Interactions of Membrane Proteins

21 January 2018

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Folding and association of a homotetrameric protein complex in an all-atom Go model

21 January 2018

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Self-assembly of transmembrane helices of bacteriorhodopsin by a replica-exchange Monte Carlo simulation

21 January 2018

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The Native GCN4 Leucine-Zipper Domain Does Not Uniquely Specify a Dimeric Oligomerization State

21 January 2018

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Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape

21 January 2018

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Replica exchange with solute tempering: a method for sampling biological systems in explicit water

21 January 2018

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Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration

21 January 2018

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A Hamiltonian Replica Exchange Approach and Its Application to the Study of Side-Chain Type and Neighbor Effects on Peptide Backbone Conformations

21 January 2018

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Combining Elastic Network Analysis and Molecular Dynamics Simulations by Hamiltonian Replica Exchange

21 January 2018

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Reordering hydrogen bonds using hamiltonian replica exchange enhances sampling of conformational changes in biomolecular systems

21 January 2018

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Replica-exchange method in van der Waals radius space: overcoming steric restrictions for biomolecules.

21 January 2018

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Constant pH replica exchange molecular dynamics in biomolecules using a discrete protonation model

21 January 2018

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On easy implementation of a variant of the replica exchange with solute tempering in GROMACS.

21 January 2018

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Replica exchange with solute scaling: a more efficient version of replica exchange with solute tempering (REST2).

21 January 2018

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Folding helical proteins in explicit solvent using dihedral-biased tempering

21 January 2018

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Hamiltonian replica exchange in GROMACS: a flexible implementation

21 January 2018

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Replica exchange with solute tempering: efficiency in large scale systems

21 January 2018

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A Second Look at Canonical Sampling of Biomolecules using Replica Exchange Simulation

21 January 2018

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Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations

21 January 2018

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Exploring the protein G helix free-energy surface by solute tempering metadynamics.

21 January 2018

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Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble

21 January 2018

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A bias-exchange approach to protein folding

21 January 2018

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String method for the study of rare events

21 January 2018

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String method in collective variables: minimum free energy paths and isocommittor surfaces.

21 January 2018

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All-atom structural models of insulin binding to the insulin receptor in the presence of a tandem hormone-binding element.

21 January 2018

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Free energy of conformational transition paths in biomolecules: the string method and its application to myosin VI.

21 January 2018

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Energetics and mechanism of the normal-to-amyloidogenic isomerization of β2-microglobulin: on-the-fly string method calculations

21 January 2018

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Toward an Automatic Determination of Enzymatic Reaction Mechanisms and Their Activation Free Energies.

21 January 2018

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On-the-fly free energy parameterization via temperature accelerated molecular dynamics

21 January 2018

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Heating and flooding: a unified approach for rapid generation of free energy surfaces.

21 January 2018

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Scalable molecular dynamics with NAMD

21 January 2018

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GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

21 January 2018

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The Amber biomolecular simulation programs

21 January 2018

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CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

21 January 2018

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Using collective variables to drive molecular dynamics simulations

21 January 2018

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PLUMED: A portable plugin for free-energy calculations with molecular dynamics

21 January 2018

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The role of water in host-guest interaction

21 January 2018

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Atomistic simulations of calcium uranyl(VI) carbonate adsorption on calcite and stepped-calcite surfaces

21 January 2018

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Protein Folding and Ligand-Enzyme Binding from Bias-Exchange Metadynamics Simulations

21 January 2018

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Assessing the Accuracy of Metadynamics†

21 January 2018

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journals/entropy/AbramsB14

21 January 2018

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DBLP Dataset 2021-01-02