(Q57943282)

April 2022 Public Data File from Crossref

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cites work

Adaptive biasing force method for scalar and vector free energy calculations

1 reference

Escaping free-energy minima

21 January 2018

1 reference

Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force

21 January 2018

1 reference

Free energy barrier for molecular motions in bistable [2]rotaxane molecular electronic devices

21 January 2018

1 reference

Thermodynamics of catalytic formation of dimethyl ether from methanol in acidic zeolites

21 January 2018

1 reference

Aspects of glycosidic bond formation in aqueous solution: chemical bonding and the role of water.

21 January 2018

1 reference

The role of water in silicate oligomerization reaction.

21 January 2018

1 reference

Entropy effects in hydrocarbon conversion reactions: free-energy integrations and transition-path sampling

21 January 2018

1 reference

How does ammonium dynamically interact with benzene in aqueous media? A first principle study using the Car-Parrinello molecular dynamics method

21 January 2018

1 reference

Free energy of binding of a small molecule to an amorphous polymer in a solvent

21 January 2018

1 reference

FMO-MD simulations on the hydration of formaldehyde in water solution with constraint dynamics

21 January 2018

1 reference

Peptide backbone sampling convergence with the adaptive biasing force algorithm

21 January 2018

1 reference

Permeation of nucleosides through lipid bilayers

21 January 2018

1 reference

Thermodynamic analysis of protegrin-1 insertion and permeation through a lipid bilayer

21 January 2018

1 reference

Uptake and Translocation Mechanisms of Cationic Amino Derivatives Functionalized on Pristine C60by Lipid Membranes: A Molecular Dynamics Simulation Study

21 January 2018

1 reference

Insertion of short amino-functionalized single-walled carbon nanotubes into phospholipid bilayer occurs by passive diffusion

21 January 2018

1 reference

Association of nicotinic acid with a poly(amidoamine) dendrimer studied by molecular dynamics simulations

21 January 2018

1 reference

Molecular dynamics simulation of the antiamoebin ion channel: linking structure and conductance.

21 January 2018

1 reference

Molecular dynamics investigation of Cl- and water transport through a eukaryotic CLC transporter

21 January 2018

1 reference

Ammonium transporters achieve charge transfer by fragmenting their substrate.

21 January 2018

1 reference

Reversal of ion-charge selectivity renders the pentameric ligand-gated ion channel GLIC insensitive to anaesthetics

21 January 2018

1 reference

Computational prediction of ionic liquid 1-octanol/water partition coefficients.

21 January 2018

1 reference

Nucleotide-dependent mechanism of Get3 as elucidated from free energy calculations

21 January 2018

1 reference

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

21 January 2018

1 reference

Umbrella integration in two or more reaction coordinates

21 January 2018

1 reference

Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics.

21 January 2018

1 reference

Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics

21 January 2018

1 reference

Using enhanced sampling and structural restraints to refine atomic structures into low-resolution electron microscopy maps

21 January 2018

1 reference

Enhanced sampling and overfitting analyses in structural refinement of nucleic acids into electron microscopy maps

21 January 2018

1 reference

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

21 January 2018

1 reference

"DFG-flip" in the insulin receptor kinase is facilitated by a helical intermediate state of the activation loop.

21 January 2018

1 reference

Mapping the network of pathways of CO diffusion in myoglobin

21 January 2018

1 reference

A computational study of water and CO migration sites and channels inside myoglobin

21 January 2018

1 reference

Single-sweep methods for free energy calculations

21 January 2018

1 reference

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

21 January 2018

1 reference

Bridging the gap between thermodynamic integration and umbrella sampling provides a novel analysis method: "Umbrella integration".

21 January 2018

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21 January 2018

1 reference

Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model.

21 January 2018

1 reference

Free energy and structural pathways of base flipping in a DNA GCGC containing sequence.

21 January 2018

1 reference

Water-mediated conformations of the alanine dipeptide as revealed by distributed umbrella sampling simulations, quantum mechanics based calculations, and experimental data

21 January 2018

1 reference

Conformational Analysis of Oligoarabinofuranosides: Overcoming Torsional Barriers with Umbrella Sampling.

21 January 2018

1 reference

Reaction path and free energy calculations of the transition between alternate conformations of HIV-1 protease

21 January 2018

1 reference

Structure of gramicidin a in a lipid bilayer environment determined using molecular dynamics simulations and solid-state NMR data

21 January 2018

1 reference

A molecular trajectory of α-actinin activation

21 January 2018

1 reference

A dynamic structural model of expanded RNA CAG repeats: a refined X-ray structure and computational investigations using molecular dynamics and umbrella sampling simulations

21 January 2018

1 reference

Probing the initial stage of aggregation of the Abeta(10-35)-protein: assessing the propensity for peptide dimerization

21 January 2018

1 reference

Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. V. Like-charged side chains

21 January 2018

1 reference

Diffusion and aggregation of sodium fluorescein in aqueous solutions

21 January 2018

1 reference

Probing pH-dependent dissociation of HdeA dimers

21 January 2018

1 reference

Structural determinants of the supramolecular organization of G protein-coupled receptors in bilayers.

21 January 2018

1 reference

Why the Drosophila Shaker K+ channel is not a good model for ligand binding to voltage-gated Kv1 channels.

21 January 2018

1 reference

Free Energy Landscape of A-DNA to B-DNA Conversion in Aqueous Solution

21 January 2018

1 reference

Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations

21 January 2018

1 reference

Potential of mean force of polyethylenimine-mediated DNA attraction

21 January 2018

1 reference

Molecular simulation study of cooperativity in hydrophobic association

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

Affinity and selectivity of ShK toxin for the Kv1 potassium channels from free energy simulations

21 January 2018

1 reference

Conserved functional surface of antimammalian scorpion β-toxins

21 January 2018

1 reference

GDP release preferentially occurs on the phosphate side in heterotrimeric G-proteins

21 January 2018

1 reference

Binding energies of five molecular pincers calculated by explicit and implicit solvent models.

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

Partitioning of 2,6-Bis(1H-Benzimidazol-2-yl)pyridine fluorophore into a phospholipid bilayer: complementary use of fluorescence quenching studies and molecular dynamics simulations

21 January 2018

1 reference

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

21 January 2018

1 reference

Convergence of Free Energy Profile of Coumarin in Lipid Bilayer

21 January 2018

1 reference

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

21 January 2018

1 reference

Effect of tension and curvature on the chemical potential of lipids in lipid aggregates

21 January 2018

1 reference

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

21 January 2018

1 reference

Taste of sugar at the membrane: thermodynamics and kinetics of the interaction of a disaccharide with lipid bilayers

21 January 2018

1 reference

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

21 January 2018

1 reference

Free energy profiles for H+ conduction along hydrogen-bonded chains of water molecules

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

Mutational effects on the catalytic mechanism of cellobiohydrolase I from Trichoderma reesei.

21 January 2018

1 reference

Mechanism of C-terminal intein cleavage in protein splicing from QM/MM molecular dynamics simulations.

21 January 2018

1 reference

Determinants of reactivity and selectivity in soluble epoxide hydrolase from quantum mechanics/molecular mechanics modeling.

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

Extracellular blockade of K(+) channels by TEA: results from molecular dynamics simulations of the KcsA channel

21 January 2018

1 reference

Gramicidin A channel as a test ground for molecular dynamics force fields

21 January 2018

1 reference

Mechanism of selectivity in aquaporins and aquaglyceroporins.

21 January 2018

1 reference

Water permeation dynamics of AqpZ: a tale of two states.

21 January 2018

1 reference

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

21 January 2018

1 reference

On the selective ion binding hypothesis for potassium channels

21 January 2018

1 reference

Theory and simulation of ion conduction in the pentameric GLIC channel

21 January 2018

1 reference

Local elevation: a method for improving the searching properties of molecular dynamics simulation.

21 January 2018

1 reference

Equilibrium Free Energies from Nonequilibrium Metadynamics

21 January 2018

1 reference

Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics.

21 January 2018

1 reference

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

21 January 2018

1 reference

Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics.

21 January 2018

1 reference

Metadynamics with Adaptive Gaussians.

21 January 2018

1 reference

Adenosine triphosphate hydrolysis mechanism in kinesin studied by combined quantum-mechanical/molecular-mechanical metadynamics simulations

21 January 2018

1 reference

Ensemble of transition state structures for the cis-trans isomerization of N-methylacetamide

21 January 2018

1 reference

Mechanism of action of cyclophilin a explored by metadynamics simulations

21 January 2018

1 reference

Trans-cis switching mechanisms in proline analogues and their relevance for the gating of the 5-HT3 receptor.

21 January 2018

1 reference

Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics.

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

Multidimensional view of amyloid fibril nucleation in atomistic detail.

21 January 2018

1 reference

Flexible docking in solution using metadynamics

21 January 2018

1 reference

Locating binding poses in protein-ligand systems using reconnaissance metadynamics

21 January 2018

1 reference

Funnel metadynamics as accurate binding free-energy method

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction

21 January 2018

1 reference

Towards the prediction of order parameters from molecular dynamics simulations in proteins

21 January 2018

1 reference

From the Cover: Simplifying the representation of complex free-energy landscapes using sketch-map

21 January 2018

1 reference

A self-learning algorithm for biased molecular dynamics

21 January 2018

1 reference

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

21 January 2018

1 reference

Reconstructing the density of states by history-dependent metadynamics.

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

From A to B in free energy space.

21 January 2018

1 reference

Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap.

21 January 2018

1 reference

Optimization by Simulated Annealing

21 January 2018

1 reference

Choosing weights for simulated tempering

21 January 2018

1 reference

Replica-exchange molecular dynamics method for protein folding

21 January 2018

1 reference

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

21 January 2018

1 reference

Virtual-Move Parallel Tempering

21 January 2018

1 reference

Asynchronous replica exchange for molecular simulations

21 January 2018

1 reference

Thermostat artifacts in replica exchange molecular dynamics simulations

21 January 2018

1 reference

Exchange Often and Properly in Replica Exchange Molecular Dynamics

21 January 2018

1 reference

Predicting the signaling state of photoactive yellow protein

21 January 2018

1 reference

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

21 January 2018

1 reference

Trp-cage: Folding free energy landscape in explicit water

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

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

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

Folding helical proteins in explicit solvent using dihedral-biased tempering

21 January 2018

1 reference

Hamiltonian replica exchange in GROMACS: a flexible implementation

21 January 2018

1 reference

Replica exchange with solute tempering: efficiency in large scale systems

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

A bias-exchange approach to protein folding

21 January 2018

1 reference

String method for the study of rare events

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

Scalable molecular dynamics with NAMD

21 January 2018

1 reference

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

21 January 2018

1 reference

The Amber biomolecular simulation programs

21 January 2018

1 reference

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

21 January 2018

1 reference

Using collective variables to drive molecular dynamics simulations

21 January 2018

1 reference

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

21 January 2018

1 reference

The role of water in host-guest interaction

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

Assessing the Accuracy of Metadynamics†

21 January 2018

1 reference

journals/entropy/AbramsB14

21 January 2018

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DBLP Dataset 2021-01-02