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The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask

https://doi.org/10.1021/jp506633n
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Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/cphc.200400669openalex-snapshot
Blue Moon Sampling, Vectorial Reaction Coordinates, and Unbiased Constrained Dynamics
inferredcites →https://doi.org/10.1002/jcc.10369openalex-snapshot
Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods
inferredcites →https://doi.org/10.1002/jcc.20289openalex-snapshot
Scalable molecular dynamics with NAMD
inferredcites →https://doi.org/10.1002/jcc.20652openalex-snapshot
Characterization of conformational equilibria through Hamiltonian and temperature replica‐exchange simulations: Assessing entropic and environmental effects
inferredcites →https://doi.org/10.1002/jcc.21285openalex-snapshot
Using multistate free energy techniques to improve the efficiency of replica exchange accelerated molecular dynamics
inferredcites →https://doi.org/10.1002/wcms.1157openalex-snapshot
Frontiers in free‐energy calculations of biological systems
inferredcites →https://doi.org/10.1007/978-3-540-38448-9openalex-snapshot
Free Energy Calculations
inferredcites →https://doi.org/10.1007/978-3-642-58360-5_2openalex-snapshot
Steered Molecular Dynamics
inferredcites →https://doi.org/10.1007/bf00124016openalex-snapshot
Local elevation: A method for improving the searching properties of molecular dynamics simulation
inferredcites →https://doi.org/10.1007/s00205-011-0426-yopenalex-snapshot
Long-Time Convergence of an Adaptive Biasing Force Method: The Bi-Channel Case
inferredcites →https://doi.org/10.1007/s00339-005-3360-8openalex-snapshot
Bayesian inference in surface physics
inferredcites →https://doi.org/10.1007/s00365-009-9071-1openalex-snapshot
Results and Questions on a Nonlinear Approximation Approach for Solving High-dimensional Partial Differential Equations
inferredcites →https://doi.org/10.1007/s11222-011-9257-9openalex-snapshot
Free energy methods for Bayesian inference: efficient exploration of univariate Gaussian mixture posteriors
inferredcites →https://doi.org/10.1016/0009-2614(92)85971-copenalex-snapshot
Holonomic constraint contributions to free energy differences from thermodynamic integration molecular dynamics simulations
inferredcites →https://doi.org/10.1016/0010-4655(95)00053-iopenalex-snapshot
The calculation of the potential of mean force using computer simulations
inferredcites →https://doi.org/10.1016/0021-9991(77)90121-8openalex-snapshot
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
inferredcites →https://doi.org/10.1016/0021-9991(83)90014-1openalex-snapshot
Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations
inferredcites →https://doi.org/10.1016/j.bpc.2006.03.019openalex-snapshot
Diffusion constant of K+ inside Gramicidin A: A comparative study of four computational methods
inferredcites →https://doi.org/10.1016/j.bpj.2011.03.054openalex-snapshot
Molecular Dynamics Simulation of the Antiamoebin Ion Channel: Linking Structure and Conductance
inferredcites →https://doi.org/10.1016/j.bpj.2012.01.063openalex-snapshot
A Bayesian Inference Scheme to Extract Diffusivity and Potential Fields from Confined Single-Molecule Trajectories
inferredcites →https://doi.org/10.1016/j.cplett.2005.07.084openalex-snapshot
Transition pathways in complex systems: Reaction coordinates, isocommittor surfaces, and transition tubes
inferredcites →https://doi.org/10.1016/s0006-3495(97)78804-0openalex-snapshot
Molecular dynamics study of unbinding of the avidin-biotin complex
inferredcites →https://doi.org/10.1016/s0009-2614(01)01397-5openalex-snapshot
Overcoming finite-sampling errors in fast-switching free-energy estimates: extrapolative analysis of a molecular system
inferredcites →https://doi.org/10.1016/s0009-2614(89)87314-2openalex-snapshot
Constrained reaction coordinate dynamics for the simulation of rare events
inferredcites →https://doi.org/10.1016/s0009-2614(99)01123-9openalex-snapshot
Replica-exchange molecular dynamics method for protein folding
inferredcites →https://doi.org/10.1016/s0166-1280(96)04999-8openalex-snapshot
Structure and dynamics of small peptides at aqueous interfaces a multi-nanosecond molecular dynamics study
inferredcites →https://doi.org/10.1016/s0301-0104(96)00247-9openalex-snapshot
A method to calculate the probability distribution for systems with large energy barriers
inferredcites →https://doi.org/10.1016/s0378-3812(98)00274-xopenalex-snapshot
Precision and accuracy of staged free-energy perturbation methods for computing the chemical potential by molecular simulation
inferredcites →https://doi.org/10.1016/s1385-8947(99)00055-8openalex-snapshot
Accelerated molecular dynamics of infrequent events
inferredcites →https://doi.org/10.1017/s0022112095000176openalex-snapshot
Computer simulations of Brownian motion of complex systems
inferredcites →https://doi.org/10.1021/ct3008099openalex-snapshot
Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?
inferredcites →https://doi.org/10.1021/ct400273topenalex-snapshot
Efficient Determination of Protein–Protein Standard Binding Free Energies from First Principles
inferredcites →https://doi.org/10.1021/ct400925sopenalex-snapshot
Calculation of Lipid-Bilayer Permeabilities Using an Average Force
inferredcites →https://doi.org/10.1021/ct500209jopenalex-snapshot
Diffusive Models of Membrane Permeation with Explicit Orientational Freedom
inferredcites →https://doi.org/10.1021/ct900279zopenalex-snapshot
Free Energy and Kinetics of Conformational Transitions from Voronoi Tessellated Milestoning with Restraining Potentials
inferredcites →https://doi.org/10.1021/ct9004432openalex-snapshot
Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables
inferredcites →https://doi.org/10.1021/ct900524topenalex-snapshot
Potential of Mean Force Calculations: A Multiple-Walker Adaptive Biasing Force Approach
inferredcites →https://doi.org/10.1021/j100066a040openalex-snapshot
Simulation of water transport through a lipid membrane
inferredcites →https://doi.org/10.1021/j100165a045openalex-snapshot
Estimation of errors in free energy calculations due to the lag between the hamiltonian and the system configuration
inferredcites →https://doi.org/10.1021/ja050581yopenalex-snapshot
Insights into the Recognition and Association of Transmembrane α-Helices. The Free Energy of α-Helix Dimerization in Glycophorin A
inferredcites →https://doi.org/10.1021/ja070778lopenalex-snapshot
Barriers to Ion Translocation in Cationic and Anionic Receptors from the Cys-Loop Family
inferredcites →https://doi.org/10.1021/ja902531kopenalex-snapshot
Permeation of Membranes by Ribose and Its Diastereomers
inferredcites →https://doi.org/10.1021/jp045546copenalex-snapshot
Automatic Method for Identifying Reaction Coordinates in Complex Systems
inferredcites →https://doi.org/10.1021/jp056751aopenalex-snapshot
Molecular Dynamics Study of the Inclusion of Cholesterol into Cyclodextrins
inferredcites →https://doi.org/10.1021/jp062755jopenalex-snapshot
Self-healing Umbrella Sampling: A Non-equilibrium Approach for Quantitative Free Energy Calculations
inferredcites →https://doi.org/10.1021/jp075308sopenalex-snapshot
Energetics of Ion Transport in a Peptide Nanotube
inferredcites →https://doi.org/10.1021/jp100926hopenalex-snapshot
Free Energy Calculations: An Efficient Adaptive Biasing Potential Method
inferredcites →https://doi.org/10.1021/jp102971xopenalex-snapshot
Good Practices in Free-Energy Calculations
inferredcites →https://doi.org/10.1021/jp4088223openalex-snapshot
Water Conduction through a Peptide Nanotube
inferredcites →https://doi.org/10.1021/jp803635eopenalex-snapshot
Binless Estimation of the Potential of Mean Force
inferredcites →https://doi.org/10.1023/a:1023208217925openalex-snapshot
Nonequilibrium Measurements of Free Energy Differences for Microscopically Reversible Markovian Systems
inferredcites →https://doi.org/10.1039/c1cp21541hopenalex-snapshot
Diffusion models of protein folding
inferredcites →https://doi.org/10.1039/df9674300040openalex-snapshot
Calculation of thermodynamic properties of liquid argon from Lennard-Jones parameters by a Monte Carlo method
inferredcites →https://doi.org/10.1051/m2an/2010044openalex-snapshot
Existence, uniqueness and convergence of a particle approximation for the Adaptive Biasing Force process
inferredcites →https://doi.org/10.1063/1.1308516openalex-snapshot
Multidimensional replica-exchange method for free-energy calculations
inferredcites →https://doi.org/10.1063/1.1359181openalex-snapshot
Accuracy of free-energy perturbation calculations in molecular simulation. I. Modeling
inferredcites →https://doi.org/10.1063/1.1405449openalex-snapshot
Accuracy of free-energy perturbation calculations in molecular simulation. II. Heuristics
inferredcites →https://doi.org/10.1063/1.1410978openalex-snapshot
Calculating free energies using average force
inferredcites →https://doi.org/10.1063/1.1590311openalex-snapshot
Free energy calculation from steered molecular dynamics simulations using Jarzynski’s equality
inferredcites →https://doi.org/10.1063/1.1642607openalex-snapshot
Assessing the efficiency of free energy calculation methods
inferredcites →https://doi.org/10.1063/1.1678245openalex-snapshot
Monte Carlo Estimation of the Free Energy by Multistage Sampling
inferredcites →https://doi.org/10.1063/1.1699114openalex-snapshot
Equation of State Calculations by Fast Computing Machines
inferredcites →https://doi.org/10.1063/1.1701695openalex-snapshot
Machine Calculation of Thermodynamic Properties of a Simple Fluid at Supercritical Temperatures
inferredcites →https://doi.org/10.1063/1.1740409openalex-snapshot
High-Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases
inferredcites →https://doi.org/10.1063/1.1749657openalex-snapshot
Statistical Mechanics of Fluid Mixtures
inferredcites →https://doi.org/10.1063/1.1773132openalex-snapshot
Overcoming free energy barriers using unconstrained molecular dynamics simulations
inferredcites →https://doi.org/10.1063/1.1877132openalex-snapshot
Solvation free energies of amino acid side chain analogs for common molecular mechanics water models
inferredcites →https://doi.org/10.1063/1.2138694openalex-snapshot
Exploring the free-energy landscape of a short peptide using an average force
inferredcites →https://doi.org/10.1063/1.2711185openalex-snapshot
Computation of free energy profiles with parallel adaptive dynamics
inferredcites →https://doi.org/10.1063/1.2829861openalex-snapshot
Adaptive biasing force method for scalar and vector free energy calculations
inferredcites →https://doi.org/10.1063/1.2844595openalex-snapshot
Adaptively biased molecular dynamics for free energy calculations
inferredcites →https://doi.org/10.1063/1.2969761openalex-snapshot
Optimal Langevin modeling of out-of-equilibrium molecular dynamics simulations
inferredcites →https://doi.org/10.1063/1.3058436openalex-snapshot
Multidimensional Langevin modeling of biomolecular dynamics
inferredcites →https://doi.org/10.1063/1.3242285openalex-snapshot
Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages
inferredcites →https://doi.org/10.1063/1.3701175openalex-snapshot
Theory of binless multi-state free energy estimation with applications to protein-ligand binding
inferredcites →https://doi.org/10.1063/1.436761openalex-snapshot
Brownian dynamics with hydrodynamic interactions
inferredcites →https://doi.org/10.1063/1.449208openalex-snapshot
Monte Carlo simulation of differences in free energies of hydration
inferredcites →https://doi.org/10.1063/1.462133openalex-snapshot
New approach to Monte Carlo calculation of the free energy: Method of expanded ensembles
inferredcites →https://doi.org/10.1063/1.464453openalex-snapshot
Determining the contributions of constraints in free energy calculations: Development, characterization, and recommendations
inferredcites →https://doi.org/10.1063/1.472109openalex-snapshot
λ-dynamics: A new approach to free energy calculations
inferredcites →https://doi.org/10.1063/1.477019openalex-snapshot
The calculation of free-energy differences by constrained molecular-dynamics simulations
inferredcites →https://doi.org/10.1063/1.477419openalex-snapshot
Free energy from constrained molecular dynamics
inferredcites →https://doi.org/10.1063/1.480139openalex-snapshot
Determination of equilibrium properties of biomolecular systems using multidimensional adaptive umbrella sampling
inferredcites →https://doi.org/10.1063/1.481329openalex-snapshot
Thermodynamic integration of the free energy along a reaction coordinate in Cartesian coordinates
inferredcites →https://doi.org/10.1063/1.4830403openalex-snapshot
Modeling and enhanced sampling of molecular systems with smooth and nonlinear data-driven collective variables
inferredcites →https://doi.org/10.1063/1.4866448openalex-snapshot
Recovering position-dependent diffusion from biased molecular dynamics simulations
inferredcites →https://doi.org/10.1063/1.4866811openalex-snapshot
Free energy calculations from adaptive molecular dynamics simulations with adiabatic reweighting
inferredcites →https://doi.org/10.1063/1.882103openalex-snapshot
An Introduction to Error Analysis: The Study of Uncertainties in Physical Measurements
inferredcites →https://doi.org/10.1073/pnas.0408098102openalex-snapshot
Reaction coordinates and rates from transition paths
inferredcites →https://doi.org/10.1073/pnas.0810631106openalex-snapshot
Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems
inferredcites →https://doi.org/10.1073/pnas.202427399openalex-snapshot
Escaping free-energy minima
inferredcites →https://doi.org/10.1073/pnas.85.7.2029openalex-snapshot
Diffusion in a rough potential.
inferredcites →https://doi.org/10.1073/pnas.91.24.11631openalex-snapshot
Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer.
inferredcites →https://doi.org/10.1080/00268976.2013.813594openalex-snapshot
Using collective variables to drive molecular dynamics simulations
inferredcites →https://doi.org/10.1080/08927020211975openalex-snapshot
Calculating Free Energies Using a Scaled-Force Molecular Dynamics Algorithm
inferredcites →https://doi.org/10.1088/0034-4885/66/9/202openalex-snapshot
Bayesian inference in physics: case studies
inferredcites →https://doi.org/10.1088/0953-8984/12/8a/316openalex-snapshot
Transition path sampling: throwing ropes over mountains in the dark
inferredcites →https://doi.org/10.1088/1367-2630/7/1/034openalex-snapshot
Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations
inferredcites →https://doi.org/10.1090/s0025-5718-2015-02952-4openalex-snapshot
Convergence of the Wang-Landau algorithm
inferredcites →https://doi.org/10.1093/amrx/abu003openalex-snapshot
Efficiency of the Wang-Landau Algorithm: A Simple Test Case
inferredcites →https://doi.org/10.1103/physreve.52.2893openalex-snapshot
Predicting slow structural transitions in macromolecular systems: Conformational flooding
inferredcites →https://doi.org/10.1103/physreve.64.056101openalex-snapshot
Determining the density of states for classical statistical models: A random walk algorithm to produce a flat histogram
inferredcites →https://doi.org/10.1103/physreve.78.051913openalex-snapshot
Calculating free-energy profiles in biomolecular systems from fast nonequilibrium processes
inferredcites →https://doi.org/10.1103/physreve.86.036707openalex-snapshot
Calculating diffusion and permeability coefficients with the oscillating forward-reverse method
inferredcites →https://doi.org/10.1103/physrevlett.100.020603openalex-snapshot
Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
inferredcites →https://doi.org/10.1103/physrevlett.57.2607openalex-snapshot
Replica Monte Carlo Simulation of Spin-Glasses
inferredcites →https://doi.org/10.1103/physrevlett.78.2690openalex-snapshot
Nonequilibrium Equality for Free Energy Differences
inferredcites →https://doi.org/10.1103/physrevlett.78.3908openalex-snapshot
Hyperdynamics: Accelerated Molecular Dynamics of Infrequent Events
inferredcites →https://doi.org/10.1103/physrevlett.86.2050openalex-snapshot
Efficient, Multiple-Range Random Walk Algorithm to Calculate the Density of States
inferredcites →https://doi.org/10.1103/physrevlett.89.180602openalex-snapshot
Theory of a Systematic Computational Error in Free Energy Differences
inferredcites →https://doi.org/10.1103/physrevlett.91.140601openalex-snapshot
Equilibrium Free Energies from Nonequilibrium Measurements Using Maximum-Likelihood Methods
inferredcites →https://doi.org/10.1103/physrevlett.96.090601openalex-snapshot
Equilibrium Free Energies from Nonequilibrium Metadynamics
inferredcites →https://doi.org/10.1103/physrevlett.96.100602openalex-snapshot
Optimal Estimates of Free Energies from Multistate Nonequilibrium Work Data
inferredcites →https://doi.org/10.1103/revmodphys.83.943openalex-snapshot
Bayesian inference in physics
inferredcites →https://doi.org/10.1126/science.271.5251.997openalex-snapshot
Ligand Binding: Molecular Mechanics Calculation of the Streptavidin-Biotin Rupture Force
inferredcites →https://doi.org/10.1137/10080600xopenalex-snapshot
Enhanced Sampling of Multidimensional Free-Energy Landscapes Using Adaptive Biasing Forces
inferredcites →https://doi.org/10.1142/p579openalex-snapshot
Free Energy Computations
inferredcites →https://doi.org/10.1142/p579#t=tocopenalex-snapshot
Free Energy Computations: A Mathematical Perspective
inferredcites →https://doi.org/10.1146/annurev.physchem.53.082301.113146openalex-snapshot
T RANSITION P ATH S AMPLING : Throwing Ropes Over Rough Mountain Passes, in the Dark
inferredcites →https://doi.org/10.1146/annurev.physchem.59.032607.093757openalex-snapshot
Two-Dimensional Infrared Spectroscopy of Photoswitchable Peptides
inferredcites →https://doi.org/10.1201/b16251-15openalex-snapshot
Scalable Molecular Dynamics with NAMD
inferredcites →https://doi.org/10.1209/0295-5075/19/6/002openalex-snapshot
Simulated Tempering: A New Monte Carlo Scheme
inferredcites →https://doi.org/10.1214/11-aos938openalex-snapshot
Convergence of adaptive and interacting Markov chain Monte Carlo algorithms
inferredcites →https://doi.org/10.1381/096089297765555359openalex-snapshot
Manuscript Preparation
inferredcites →https://doi.org/10.1529/biophysj.107.105528openalex-snapshot
Secondary and Tertiary Structure Elasticity of Titin Z1Z2 and a Titin Chain Model
inferredcites →https://doi.org/10.1529/biophysj.107.115105openalex-snapshot
Diffusion of Glycerol through Escherichia coli Aquaglyceroporin GlpF
inferredcites →https://doi.org/10.5802/smai-jcm.4openalex-snapshot
Long-time convergence of an adaptive biasing force method: Variance reduction by Helmholtz projection
inferredcites →https://doi.org/10.5860/choice.35-2173openalex-snapshot
An introduction to error analysis: the study of uncertainties in physical measurements

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inferred← citeshttps://doi.org/10.2139/ssrn.3416843openalex-extracted
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inferred← citeshttps://doi.org/10.1002/9783527806836.ch10openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/9783527830503.ch8openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/adts.201800191openalex-snapshot
Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations
inferred← citeshttps://doi.org/10.1002/adts.202300080openalex-snapshot
Cocrystal Growth in Organic Semiconductor Thin Films: Simulation of Pentacene, Perfluoropentacene, and Their 1:1 Blend Deposited On Graphite
inferred← citeshttps://doi.org/10.1002/aic.16567openalex-snapshot
Effects of glycol on adsorption dynamics of idealized water droplets on LTA‐3A zeolite surfaces
inferred← citeshttps://doi.org/10.1002/aic.16728openalex-snapshot
Adsorption characteristics of glycols on calcite and hematite
inferred← citeshttps://doi.org/10.1002/chem.201702756openalex-snapshot
Understanding Noncovalent Interactions of Small Molecules with Carbon Nanotubes
inferred← citeshttps://doi.org/10.1002/cjoc.201500402openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/cphc.202000472openalex-snapshot
A Photochemical/Thermal Switch Based on 4,4′‐Bis(benzimidazolio)stilbene: Synthesis and Supramolecular Properties.
inferred← citeshttps://doi.org/10.1002/jcc.24275openalex-snapshot
Toward the identification of molecular cogs
inferred← citeshttps://doi.org/10.1002/jcc.24738openalex-snapshot
Rigidity and flexibility in the tetrasaccharide linker of proteoglycans from atomic‐resolution molecular simulation
inferred← citeshttps://doi.org/10.1002/jcc.26063openalex-snapshot
Modulation of membrane permeability by carbon dioxide
inferred← citeshttps://doi.org/10.1002/jcc.26098openalex-snapshot
A Minimal Membrane Metal Transport System: Dynamics and Energetics of mer Proteins
inferred← citeshttps://doi.org/10.1002/jcc.26382openalex-snapshot
Free‐energy calculations of the host–guest association in grafted supramolecular assemblies
inferred← citeshttps://doi.org/10.1002/jcc.26727openalex-snapshot
Mean force based temperature accelerated sliced sampling: Efficient reconstruction of high dimensional free energy landscapes
inferred← citeshttps://doi.org/10.1002/jcc.26882openalex-snapshot
Exploration of high dimensional free energy landscapes by a combination of temperature‐accelerated sliced sampling and parallel biasing
inferred← citeshttps://doi.org/10.1002/jcc.70110openalex-snapshot
On the Use of PDB X‐Ray Crystal Structures as Force Field Target and Validation Data for Pyranose Ring Puckering
inferred← citeshttps://doi.org/10.1002/jcc.70359openalex-snapshot
ASH : A Multi‐Scale, Multi‐Theory Modeling Program
inferred← citeshttps://doi.org/10.1002/macp.202500499openalex-snapshot
Triggered Dissolution of Electrostatically Crosslinked Hydrogels from Star‐Shaped Polyampholytic Block Copolymers
inferred← citeshttps://doi.org/10.1002/minf.201501018openalex-snapshot
Binding Kinetics in Drug Discovery
inferred← citeshttps://doi.org/10.1002/pro.4446openalex-snapshot
CHARMM‐GUI Enhanced Sampler for various collective variables and enhanced sampling methods
inferred← citeshttps://doi.org/10.1002/prot.25611openalex-snapshot
Computational study on the selective inhibition mechanism of MS402 to the first and second bromodomains of BRD4
inferred← citeshttps://doi.org/10.1002/slct.201601160openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/wcms.1306openalex-snapshot
Molecular ‘time‐machines’ to unravel key biological events for drug design
inferred← citeshttps://doi.org/10.1002/wcms.1329openalex-snapshot
Reaction coordinates and transition states in enzymatic catalysis
inferred← citeshttps://doi.org/10.1002/wcms.1398openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/wcms.1448openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/wcms.1689openalex-snapshot
Computational biophysics meets cryo‐EM revolution in the search for the functional dynamics of biomolecular systems
inferred← citeshttps://doi.org/10.1002/wcms.70082openalex-snapshot
Deep Learning for Protein Modeling: From Single Structure to Bound Complex and Thermodynamic Ensemble, With a Focus on Architectural Design
inferred← citeshttps://doi.org/10.1007/978-1-0716-1468-6_10openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-1-0716-1855-4_15openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-1-4939-7756-7_17openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-3-031-73730-5_1openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s00214-015-1792-6openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s00214-018-2376-zopenalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s00245-023-10075-5openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s10822-017-0085-7openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s10822-018-0164-4openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s10822-020-00295-0openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/b978-0-12-409547-2.12344-3openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/b978-0-12-814531-9.00002-6openalex-snapshot
Computational modeling of the adsorption of capping agent biomolecules to inorganic nanoparticles
inferred← citeshttps://doi.org/10.1016/b978-0-12-821978-2.00112-4openalex-snapshot
Equilibrium and Nonequilibrium Methods for Free-Energy Calculations With Molecular Dynamics
inferred← citeshttps://doi.org/10.1016/b978-0-12-821978-2.00138-0openalex-snapshot
Quantum Chemical and Informatics-Based Approaches for Probing Biomolecular Systems Toxicology
inferred← citeshttps://doi.org/10.1016/b978-0-32-388440-2.00015-0openalex-snapshot
Free energy and enhanced sampling
inferred← citeshttps://doi.org/10.1016/b978-0-32-388440-2.00023-xopenalex-snapshot
References
inferred← citeshttps://doi.org/10.1016/b978-0-323-90995-2.00016-3openalex-snapshot
In silico approaches to biomacromolecules through conformational dynamics and catalysis
inferred← citeshttps://doi.org/10.1016/b978-0-323-95917-9.00008-0openalex-snapshot
Enhanced sampling
inferred← citeshttps://doi.org/10.1016/b978-0-44-456349-1.00011-8openalex-snapshot
Landau free energies and restricted averages
inferred← citeshttps://doi.org/10.1016/b978-0-443-29808-0.00028-5openalex-snapshot
Recent progress in free energy methods
inferred← citeshttps://doi.org/10.1016/b978-0-443-36518-8.00025-4openalex-snapshot
Computational approaches in antimicrobial drug discovery
inferred← citeshttps://doi.org/10.1016/bs.arcc.2022.09.004openalex-snapshot
Assessing entropy for catalytic processes at complex reactive interfaces
inferred← citeshttps://doi.org/10.1016/j.amc.2024.128683openalex-snapshot
Computational efficiency study of a micro-macro Markov chain Monte Carlo method for molecular dynamics
inferred← citeshttps://doi.org/10.1016/j.bbamem.2015.12.020openalex-snapshot
Simulations of outer membrane channels and their permeability
inferred← citeshttps://doi.org/10.1016/j.bbamem.2016.02.017openalex-snapshot
Decrypting protein insertion through the translocon with free-energy calculations
inferred← citeshttps://doi.org/10.1016/j.bbamem.2021.183763openalex-snapshot
Molecular dynamics simulations of doxorubicin in sphingomyelin-based lipid membranes
inferred← citeshttps://doi.org/10.1016/j.bbamem.2023.184120openalex-snapshot
MemCross: Accelerated Weight Histogram method to assess membrane permeability
inferred← citeshttps://doi.org/10.1016/j.bios.2022.114360openalex-snapshot
Computer simulation and design of DNA-nanoprobe for fluorescence imaging DNA repair enzyme in living cells
inferred← citeshttps://doi.org/10.1016/j.bpc.2016.03.003openalex-snapshot
Molecular simulations of micellar aggregation of polysorbate 20 ester fractions and their interaction with N-phenyl-1-naphthylamine dye
inferred← citeshttps://doi.org/10.1016/j.bpc.2025.107457openalex-snapshot
Influence of local ordering in the permeation of Temozolomide through the brain plasmatic membrane
inferred← citeshttps://doi.org/10.1016/j.bpj.2020.01.044openalex-snapshot
Coexistence of Lipid Phases Stabilizes Interstitial Water in the Outer Layer of Mammalian Skin
inferred← citeshttps://doi.org/10.1016/j.bpj.2020.08.015openalex-snapshot
Simulation Study of the Plasticity of k-Turn Motif in Different Environments
inferred← citeshttps://doi.org/10.1016/j.bpj.2020.08.031openalex-snapshot
Free Energy Landscape and Conformational Kinetics of Hoogsteen Base Pairing in DNA vs. RNA
inferred← citeshttps://doi.org/10.1016/j.bpj.2023.02.021openalex-snapshot
Path sampling with memory reduction and replica exchange to reach long permeation timescales
inferred← citeshttps://doi.org/10.1016/j.chemphys.2018.09.014openalex-snapshot
The dependence of hydrophobic interactions on solute size
inferred← citeshttps://doi.org/10.1016/j.chemphys.2021.111200openalex-snapshot
Directional nature of hydrophobic interactions: Implications for the mechanism of molecular recognition
inferred← citeshttps://doi.org/10.1016/j.chemphys.2022.111550openalex-snapshot
Temperature effects on hydrophobic interactions: Implications for protein unfolding
inferred← citeshttps://doi.org/10.1016/j.chemphyslip.2018.12.004openalex-snapshot
Dissecting the thermodynamic contributions of the charged residues in the membrane anchoring of Bcl-xl C-terminal domain
inferred← citeshttps://doi.org/10.1016/j.chom.2019.09.016openalex-snapshot
Structural Basis for Broad HIV-1 Neutralization by the MPER-Specific Human Broadly Neutralizing Antibody LN01
inferred← citeshttps://doi.org/10.1016/j.comptc.2025.115091openalex-snapshot
Caffeine as a stabilizer in Novel Hydroxypropyl-β-cyclodextrin/Axitinib Drug-Delivery Systems: A computational study
inferred← citeshttps://doi.org/10.1016/j.cplett.2018.10.066openalex-snapshot
The structural origin of hydration repulsive force
inferred← citeshttps://doi.org/10.1016/j.csbj.2022.10.039openalex-snapshot
In silico investigation and surmounting of Lipopolysaccharide barrier in Gram-Negative Bacteria: How far has molecular dynamics Come?
inferred← citeshttps://doi.org/10.1016/j.dyepig.2020.108356openalex-snapshot
Cinnamoyl–coumarin hybrid derivatives with remarkable fluorescent molecular-rotor properties in mixtures of DPPC:DOPC LUVs
inferred← citeshttps://doi.org/10.1016/j.dyepig.2024.112290openalex-snapshot
Exploring the photophysics of cinnamoyl-coumarin derivatives in cucurbit [7]uril complexes and assessing phototoxicity in HeLa cells
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2024.134945openalex-snapshot
Grb2 Y160F mutant mimics the wild-type monomeric state dynamics and the monomer-dimer equilibrium
inferred← citeshttps://doi.org/10.1016/j.ijheatmasstransfer.2023.124244openalex-snapshot
Predicting evaporation/condensation mass fluxes using a chemical kinetics framework: Pseudo-chemical potential as the activation energy
inferred← citeshttps://doi.org/10.1016/j.isci.2022.104264openalex-snapshot
Single-molecule biophysics experiments in silico: Toward a physical model of a replisome
inferred← citeshttps://doi.org/10.1016/j.jbc.2022.102627openalex-snapshot
Molecular simulation of lignin-related aromatic compound permeation through gram-negative bacterial outer membranes
inferred← citeshttps://doi.org/10.1016/j.jcp.2022.111377openalex-snapshot
Solving eigenvalue PDEs of metastable diffusion processes using artificial neural networks
inferred← citeshttps://doi.org/10.1016/j.jcp.2025.114313openalex-snapshot
Improving sampling by modifying the effective diffusion
inferred← citeshttps://doi.org/10.1016/j.molliq.2021.117157openalex-snapshot
Remdesivir interactions with sulphobutylether-β-cyclodextrins: A case study using selected substitution patterns
inferred← citeshttps://doi.org/10.1016/j.molliq.2021.117588openalex-snapshot
Aggregation versus inclusion complexes to solubilize drugs with cyclodextrins. A case study using sulphobutylether-β-cyclodextrins and remdesivir
inferred← citeshttps://doi.org/10.1016/j.petlm.2021.10.003openalex-snapshot
A zero emission scheme for producing energy from natural gas hydrates and conventional natural gas
inferred← citeshttps://doi.org/10.1016/j.petlm.2021.10.012openalex-snapshot
Routes to hydrate formation from water dissolved in gas and impact of mineral surfaces
inferred← citeshttps://doi.org/10.1016/j.polymer.2021.124267openalex-snapshot
Quantitative analysis of chiral transitions and its implication for non-classical crystallization in isotactic polypropylene
inferred← citeshttps://doi.org/10.1016/j.revip.2017.05.001openalex-snapshot
Strategies for the exploration of free energy landscapes: Unity in diversity and challenges ahead
inferred← citeshttps://doi.org/10.1016/j.sbi.2019.12.021openalex-snapshot
Understanding and modelling the interactions of peptides with membranes: from partitioning to self-assembly
inferred← citeshttps://doi.org/10.1016/j.sbi.2022.102497openalex-snapshot
Enhancing sampling with free-energy calculations
inferred← citeshttps://doi.org/10.1016/j.sbi.2024.102919openalex-snapshot
The next revolution in computational simulations: Harnessing AI and quantum computing in molecular dynamics
inferred← citeshttps://doi.org/10.1016/j.solidstatesciences.2026.108254openalex-snapshot
The seeding method: A test case for classical nucleation theory in small systems
inferred← citeshttps://doi.org/10.1016/j.surfrep.2017.02.001openalex-snapshot
Nanoparticle decoration with surfactants: Molecular interactions, assembly, and applications
inferred← citeshttps://doi.org/10.1016/j.xpro.2024.103223openalex-snapshot
Protocol for calculating binding free energy of RNA:RNA interactions through molecular dynamics simulations using adaptive biasing force technique
inferred← citeshttps://doi.org/10.1017/s0962492923000016openalex-snapshot
Overcoming the timescale barrier in molecular dynamics: Transfer operators, variational principles and machine learning
inferred← citeshttps://doi.org/10.1021/acs.accounts.5c00666openalex-snapshot
One for All, All for One: A Unified Framework for Free-Energy Calculations
inferred← citeshttps://doi.org/10.1021/acs.accounts.9b00473openalex-snapshot
Taming Rugged Free Energy Landscapes Using an Average Force
inferred← citeshttps://doi.org/10.1021/acs.biochem.0c00460openalex-snapshot
Dynamics and Mechanism of Binding of Androstenedione to Membrane-Associated Aromatase
inferred← citeshttps://doi.org/10.1021/acs.chemrev.0c00534openalex-snapshot
Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation
inferred← citeshttps://doi.org/10.1021/acs.chemrev.1c00800openalex-snapshot
Improving the Accuracy of Atomistic Simulations of the Electrochemical Interface
inferred← citeshttps://doi.org/10.1021/acs.chemrev.5c00359openalex-snapshot
Quantum Chemistry Calculations of Circularly Polarized Luminescence (CPL): From Spectral Modeling to Molecular Design
inferred← citeshttps://doi.org/10.1021/acs.chemrev.7b00139openalex-snapshot
Biointerface Structural Effects on the Properties and Applications of Bioinspired Peptide-Based Nanomaterials
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00279openalex-snapshot
Finding an Optimal Pathway on a Multidimensional Free-Energy Landscape
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00269openalex-snapshot
BFEE2: Automated, Streamlined, and Accurate Absolute Binding Free-Energy Calculations
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00613openalex-snapshot
Fighting Against Bacterial Lipopolysaccharide-Caused Infections through Molecular Dynamics Simulations: A Review
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00731openalex-snapshot
Bending of Canonical and G/T Mismatched DNAs
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c01010openalex-snapshot
MLCV: Bridging Machine-Learning-Based Dimensionality Reduction and Free-Energy Calculation
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c01543openalex-snapshot
Standard Binding Free Energy and Membrane Desorption Mechanism for a Phospholipase C
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00419openalex-snapshot
Design of Peptides that Fold and Self-Assemble on Graphite
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c01097openalex-snapshot
Free-Energy Profiles for Membrane Permeation of Compounds Calculated Using Rare-Event Sampling Methods
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c01540openalex-snapshot
Microscopic Understanding of the Conformational Stability of the Aggregated Nonamyloid β Components of α-Synuclein
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c01589openalex-snapshot
Selectivity and Ranking of Tight-Binding JAK-STAT Inhibitors Using Markovian Milestoning with Voronoi Tessellations
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00603openalex-snapshot
Targeted Protein Degradation: Advances, Challenges, and Prospects for Computational Methods
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01072openalex-snapshot
Telescoping-Solvation-Box Protocol-Based Umbrella Sampling Method for Potential Mean Force Estimation
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01257openalex-snapshot
Computational Probing of the Folding Mechanism of Human Telomeric G-Quadruplex DNA
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01705openalex-snapshot
Performance and Analysis of the Alchemical Transfer Method for Binding-Free-Energy Predictions of Diverse Ligands
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c02158openalex-snapshot
A Hybrid OPES-eABF Framework for Efficient Exploration and Data-Driven Collective Variable Discovery in Complex Free-Energy Landscapes
inferred← citeshttps://doi.org/10.1021/acs.jcim.6c00532openalex-snapshot
Functional Calmodulin States Are Selected from an Electrostatically Tuned Free Energy Landscape
inferred← citeshttps://doi.org/10.1021/acs.jcim.6c00807openalex-snapshot
TPS-Flow: Physics-Guided Flow-Based Generative Modeling of Protein Transition Paths
inferred← citeshttps://doi.org/10.1021/acs.jcim.6c01396openalex-snapshot
DIME: Dynamics Inferred from Monte Carlo Ensembles via Continuous-Time Markov Chains
inferred← citeshttps://doi.org/10.1021/acs.jcim.6c02272openalex-snapshot
Sequence Dependence of Folding and Self-Assembly of Glycine-X Repeat Peptides on Graphite
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00521openalex-snapshot
Iodide Binding in Sodium-Coupled Cotransporters
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00628openalex-snapshot
BIM Binding Remotely Regulates BAX Activation: Insights from the Free Energy Landscapes
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00115openalex-snapshot
ELF: An Extended-Lagrangian Free Energy Calculation Module for Multiple Molecular Dynamics Engines
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00974openalex-snapshot
Computational Methods Used to Explore Transport Events in Biological Systems
inferred← citeshttps://doi.org/10.1021/acs.jctc.0c00448openalex-snapshot
Position-Dependent Diffusion Constant of Molecules in Heterogeneous Systems as Evaluated by the Local Mean Squared Displacement
inferred← citeshttps://doi.org/10.1021/acs.jctc.1c00103openalex-snapshot
Overcoming Free-Energy Barriers with a Seamless Combination of a Biasing Force and a Collective Variable-Independent Boost Potential
inferred← citeshttps://doi.org/10.1021/acs.jctc.1c00369openalex-snapshot
Improved Sampling and Free Energy Estimates for Antibiotic Permeation through Bacterial Porins
inferred← citeshttps://doi.org/10.1021/acs.jctc.1c00415openalex-snapshot
Chasing Collective Variables Using Autoencoders and Biased Trajectories
inferred← citeshttps://doi.org/10.1021/acs.jctc.1c00586openalex-snapshot
Force-Correction Analysis Method for Derivation of Multidimensional Free-Energy Landscapes from Adaptively Biased Replica Simulations
inferred← citeshttps://doi.org/10.1021/acs.jctc.1c00609openalex-snapshot
Using Constrained Density Functional Theory to Track Proton Transfers and to Sample Their Associated Free Energy Surface
inferred← citeshttps://doi.org/10.1021/acs.jctc.1c00770openalex-snapshot
Gaussian-Accelerated Molecular Dynamics with the Weighted Ensemble Method: A Hybrid Method Improves Thermodynamic and Kinetic Sampling
inferred← citeshttps://doi.org/10.1021/acs.jctc.1c01049openalex-snapshot
A Companion Guide to the String Method with Swarms of Trajectories: Characterization, Performance, and Pitfalls
inferred← citeshttps://doi.org/10.1021/acs.jctc.1c01081openalex-snapshot
Human Learning for Molecular Simulations: The Collective Variables Dashboard in VMD
inferred← citeshttps://doi.org/10.1021/acs.jctc.2c00106openalex-snapshot
On Computing Equilibrium Binding Constants for Protein–Protein Association in Membranes
inferred← citeshttps://doi.org/10.1021/acs.jctc.2c00197openalex-snapshot
Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials
inferred← citeshttps://doi.org/10.1021/acs.jctc.2c01162openalex-snapshot
Simulated Tempering-Enhanced Umbrella Sampling Improves Convergence of Free Energy Calculations of Drug Membrane Permeation
inferred← citeshttps://doi.org/10.1021/acs.jctc.3c00028openalex-snapshot
Discovering Reaction Pathways, Slow Variables, and Committor Probabilities with Machine Learning
inferred← citeshttps://doi.org/10.1021/acs.jctc.3c00448openalex-snapshot
Entropy and Energy Profiles of Chemical Reactions
inferred← citeshttps://doi.org/10.1021/acs.jctc.3c00938openalex-snapshot
Improved Sampling of Adaptive Path Collective Variables by Stabilized Extended-System Dynamics
inferred← citeshttps://doi.org/10.1021/acs.jctc.3c00941openalex-snapshot
A Rigorous Framework for Calculating Protein–Protein Binding Affinities in Membranes
inferred← citeshttps://doi.org/10.1021/acs.jctc.3c00973openalex-snapshot
Free Energy Profile Decomposition Analysis for QM/MM Simulations of Enzymatic Reactions
inferred← citeshttps://doi.org/10.1021/acs.jctc.3c01186openalex-snapshot
Calculating Binding Free Energies in Model Host–Guest Systems with Unrestrained Advanced Sampling
inferred← citeshttps://doi.org/10.1021/acs.jctc.3c01249openalex-snapshot
Lambda-ABF: Simplified, Portable, Accurate, and Cost-Effective Alchemical Free-Energy Computation
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c00191openalex-snapshot
Studying the Collective Functional Response of a Receptor in Alchemical Ligand Binding Free Energy Simulations with Accelerated Solvation Layer Dynamics
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c00288openalex-snapshot
Elucidating Protein Structures in the Gas Phase: Traversing Configuration Space with Biasing Methods
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c00315openalex-snapshot
Application of Generative Artificial Intelligence in Predicting Membrane Partitioning of Drugs: Combining Denoising Diffusion Probabilistic Models and MD Simulations Reduces the Computational Cost to One-Third
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c00425openalex-snapshot
Good Rates From Bad Coordinates: The Exponential Average Time-dependent Rate Approach
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c00435openalex-snapshot
Learning Collective Variables with Synthetic Data Augmentation through Physics-Inspired Geodesic Interpolation
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c00454openalex-snapshot
Machine Learning Derived Collective Variables for the Study of Protein Homodimerization in Membrane
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c00764openalex-snapshot
Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c00776openalex-snapshot
Buckets Instead of Umbrellas for Enhanced Sampling and Free Energy Calculations
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c00878openalex-snapshot
Contact-Map-Driven Exploration of Heterogeneous Protein-Folding Paths
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c01209openalex-snapshot
Improving the Computational Efficiency of the Adaptive Biasing Force Sampling by Leveraging the Telescopic-Solvation Scheme
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c01679openalex-snapshot
Improved Free-Energy Estimates for the Permeation of Bulky Antibiotic Molecules through Porin Channels Using Temperature-Accelerated Sliced Sampling
inferred← citeshttps://doi.org/10.1021/acs.jctc.5b00405openalex-snapshot
Computational Calorimetry: High-Precision Calculation of Host–Guest Binding Thermodynamics
inferred← citeshttps://doi.org/10.1021/acs.jctc.5c00395openalex-snapshot
Combining Fast Exploration with Accurate Reweighting in the OPES-eABF Hybrid Sampling Method
inferred← citeshttps://doi.org/10.1021/acs.jctc.5c00717openalex-snapshot
Solute Tempered Adiabatic Free Energy Dynamics for Enhancing Conformational Space Sampling
inferred← citeshttps://doi.org/10.1021/acs.jctc.6b00447openalex-snapshot
Extended Adaptive Biasing Force Algorithm. An On-the-Fly Implementation for Accurate Free-Energy Calculations
inferred← citeshttps://doi.org/10.1021/acs.jctc.6c00120openalex-snapshot
Bayesian Umbrella Quadrature Automates Free-Energy Calculations Across Diverse Molecular Systems and Processes
inferred← citeshttps://doi.org/10.1021/acs.jctc.6c00439openalex-snapshot
Free-Energy Landscapes of HBV Hexamer Closure Reveal Key Structural Features of the Transition
inferred← citeshttps://doi.org/10.1021/acs.jctc.6c00645openalex-snapshot
A Residence-Time Approach for Determining Position-Dependent Diffusivities from Biased Molecular Simulations
inferred← citeshttps://doi.org/10.1021/acs.jctc.6c00879openalex-snapshot
A Force-Kernel Reformulation of the Extended-System Adaptive Biasing Force for Free-Energy Calculations
inferred← citeshttps://doi.org/10.1021/acs.jctc.7b00032openalex-snapshot
The Extended Generalized Adaptive Biasing Force Algorithm for Multidimensional Free-Energy Calculations
inferred← citeshttps://doi.org/10.1021/acs.jctc.7b00105openalex-snapshot
Free Energy of Binding and Mechanism of Interaction for the MEEVD-TPR2A Peptide–Protein Complex
inferred← citeshttps://doi.org/10.1021/acs.jctc.7b00242openalex-snapshot
Effective Conformational Sampling in Explicit Solvent with Gaussian Biased Accelerated Molecular Dynamics
inferred← citeshttps://doi.org/10.1021/acs.jctc.7b00264openalex-snapshot
Permeability of a Fluid Lipid Bilayer to Short-Chain Alcohols from First Principles
inferred← citeshttps://doi.org/10.1021/acs.jctc.7b00275openalex-snapshot
Attach-Pull-Release Calculations of Ligand Binding and Conformational Changes on the First BRD4 Bromodomain
inferred← citeshttps://doi.org/10.1021/acs.jctc.7b00791openalex-snapshot
New Coarse Variables for the Accurate Determination of Standard Binding Free Energies
inferred← citeshttps://doi.org/10.1021/acs.jctc.8b00272openalex-snapshot
Link between Membrane Composition and Permeability to Drugs
inferred← citeshttps://doi.org/10.1021/acs.jctc.8b00448openalex-snapshot
Biasing Smarter, Not Harder, by Partitioning Collective Variables into Families in Parallel Bias Metadynamics
inferred← citeshttps://doi.org/10.1021/acs.jctc.8b00830openalex-snapshot
Thermodynamics of Adsorption on Graphenic Surfaces from Aqueous Solution
inferred← citeshttps://doi.org/10.1021/acs.jctc.8b00967openalex-snapshot
Analytical Model of the Free Energy of Alchemical Molecular Binding
inferred← citeshttps://doi.org/10.1021/acs.jctc.8b01142openalex-snapshot
Potential Mean Force from Umbrella Sampling Simulations: What Can We Learn and What Is Missed?
inferred← citeshttps://doi.org/10.1021/acs.jctc.9b00022openalex-snapshot
Affordable Membrane Permeability Calculations: Permeation of Short-Chain Alcohols through Pure-Lipid Bilayers and a Mammalian Cell Membrane
inferred← citeshttps://doi.org/10.1021/acs.jctc.9b00524openalex-snapshot
Exploring Conformational Transitions and Free-Energy Profiles of Proton-Coupled Oligopeptide Transporters
inferred← citeshttps://doi.org/10.1021/acs.jctc.9b00541openalex-snapshot
Interaction of Camptothecin with Model Cellular Membranes
inferred← citeshttps://doi.org/10.1021/acs.jctc.9b00725openalex-snapshot
CL-FEP: An End-State Free Energy Perturbation Approach
inferred← citeshttps://doi.org/10.1021/acs.jctc.9b00853openalex-snapshot
Overcoming Orthogonal Barriers in Alchemical Free Energy Calculations: On the Relative Merits of λ-Variations, λ-Extrapolations, and Biasing
inferred← citeshttps://doi.org/10.1021/acs.jctc.9b01081openalex-snapshot
Reaction Path Analysis from Potential Energy Contributions Using Forces: An Accessible Estimator of Reaction Coordinate Adequacy
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.1c00580openalex-snapshot
Cyclosporin Structure and Permeability: From A to Z and Beyond
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.5b01684openalex-snapshot
Role of Molecular Dynamics and Related Methods in Drug Discovery
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.5c03315openalex-snapshot
Structural and Kinetic Basis for the Rational Design of Next-Generation β-Lactamase Inhibitors
inferred← citeshttps://doi.org/10.1021/acs.joc.0c02917openalex-snapshot
Modes of Micromolar Host–Guest Binding of β-Cyclodextrin Complexes Revealed by NMR Spectroscopy in Salt Water
inferred← citeshttps://doi.org/10.1021/acs.jpca.1c02869openalex-snapshot
Multiscale Reweighted Stochastic Embedding: Deep Learning of Collective Variables for Enhanced Sampling
inferred← citeshttps://doi.org/10.1021/acs.jpcb.0c03615openalex-snapshot
Understanding and Tracking the Excess Proton in Ab Initio Simulations; Insights from IR Spectra
inferred← citeshttps://doi.org/10.1021/acs.jpcb.0c05629openalex-snapshot
Conformational Free-Energy Landscapes of Alanine Dipeptide in Hydrated Ionic Liquids from Enhanced Sampling Methods
inferred← citeshttps://doi.org/10.1021/acs.jpcb.1c09282openalex-snapshot
Protective Mechanism of a Layer-by-Layer-Assembled Artificial Cell Wall on Probiotics
inferred← citeshttps://doi.org/10.1021/acs.jpcb.1c09423openalex-snapshot
Conformational Change from U- to I-Shape of Ion Transporters Facilitates K+ Transport across Lipid Bilayers
inferred← citeshttps://doi.org/10.1021/acs.jpcb.2c01158openalex-snapshot
Consistent Picture of Phosphate–Divalent Cation Binding from Models with Implicit and Explicit Electronic Polarization
inferred← citeshttps://doi.org/10.1021/acs.jpcb.2c04016openalex-snapshot
Salt Effect on Donnan Equilibrium in Montmorillonite Demonstrated with Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1021/acs.jpcb.3c01947openalex-snapshot
A Consistent Thermodynamic Characterization of the Adsorption Process through the Calculation of Free Energy Contributions
inferred← citeshttps://doi.org/10.1021/acs.jpcb.3c02028openalex-snapshot
Comprehensive Approach to Simulating Large Scale Conformational Changes in Biological Systems Utilizing a Path Collective Variable and New Barrier Restraint
inferred← citeshttps://doi.org/10.1021/acs.jpcb.3c02285openalex-snapshot
Molecular Dynamics Simulation Study of the Protonation State Dependence of Glutamic Acid Transport through a Cyclic Peptide Nanotube
inferred← citeshttps://doi.org/10.1021/acs.jpcb.3c03799openalex-snapshot
Using Implicit-Solvent Potentials to Extract Water Contributions to Enthalpy–Entropy Compensation in Biomolecular Associations
inferred← citeshttps://doi.org/10.1021/acs.jpcb.3c06940openalex-snapshot
Contribution of Signaling Partner Association to Strigolactone Receptor Selectivity
inferred← citeshttps://doi.org/10.1021/acs.jpcb.3c08090openalex-snapshot
Orientation and Membrane Partition Free Energy of PeT-Based Voltage-Sensitive Dyes from Molecular Simulations
inferred← citeshttps://doi.org/10.1021/acs.jpcb.4c03835openalex-snapshot
Membrane Stabilization of Helical Previtamin D Conformers as Possible Enhancement of Vitamin D Photoproduction
inferred← citeshttps://doi.org/10.1021/acs.jpcb.4c05020openalex-snapshot
Statistical Mechanical Theories of Membrane Permeability
inferred← citeshttps://doi.org/10.1021/acs.jpcb.4c05134openalex-snapshot
A Computational Study of the siRNA-Silica Nanoparticle Binding Process
inferred← citeshttps://doi.org/10.1021/acs.jpcb.4c05604openalex-snapshot
Expanded Functionality and Portability for the Colvars Library
inferred← citeshttps://doi.org/10.1021/acs.jpcb.5b00763openalex-snapshot
Journey of Poly-Nucleotides through OmpF Porin
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