Atomic-Level Characterization of the Structural Dynamics of Proteins
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October 2010 |
Characterization of conformational equilibria through Hamiltonian and temperature replica-exchange simulations: Assessing entropic and environmental effects
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January 2007 |
Escaping free-energy minima
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September 2002 |
Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
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January 2008 |
A temperature accelerated method for sampling free energy and determining reaction pathways in rare events simulations
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July 2006 |
Efficient and Direct Generation of Multidimensional Free Energy Surfaces via Adiabatic Dynamics without Coordinate Transformations
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December 2008 |
Adaptive biasing force method for scalar and vector free energy calculations
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April 2008 |
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
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February 1977 |
Constrained reaction coordinate dynamics for the simulation of rare events
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April 1989 |
Free energy from constrained molecular dynamics
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November 1998 |
High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases
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August 1954 |
Statistical Mechanics of Fluid Mixtures
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May 1935 |
Biased Sampling of Nonequilibrium Trajectories: Can Fast Switching Simulations Outperform Conventional Free Energy Calculation Methods? †
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April 2005 |
Heating and flooding: A unified approach for rapid generation of free energy surfaces
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July 2012 |
Smoothed Biasing Forces Yield Unbiased Free Energies with the Extended-System Adaptive Biasing Force Method
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December 2016 |
Transition path sampling and the calculation of rate constants
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February 1998 |
On the calculation of reaction rate constants in the transition path ensemble
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April 1999 |
A novel path sampling method for the calculation of rate constants
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May 2003 |
Rate constants for diffusive processes by partial path sampling
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March 2004 |
Multiple state transition path sampling
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December 2008 |
Sampling Rare Switching Events in Biochemical Networks
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January 2005 |
Weighted-ensemble Brownian dynamics simulations for protein association reactions
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January 1996 |
Computing time scales from reaction coordinates by milestoning
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June 2004 |
Metadynamics: Metadynamics
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February 2011 |
Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics
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March 2010 |
Temperature-Accelerated Method for Exploring Polymorphism in Molecular Crystals Based on Free Energy
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June 2011 |
Order-parameter-aided temperature-accelerated sampling for the exploration of crystal polymorphism and solid-liquid phase transitions
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June 2014 |
Microscopic mechanisms of equilibrium melting of a solid
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November 2014 |
Effects of hydration on the protonation state of a lysine analog crossing a phospholipid bilayer – insights from molecular dynamics and free-energy calculations
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January 2018 |
Exploring the free-energy landscape of a short peptide using an average force
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December 2005 |
How Do Membrane Transporters Sense pH? The Case of the Mitochondrial ADP–ATP Carrier
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October 2013 |
Affordable Membrane Permeability Calculations: Permeation of Short-Chain Alcohols through Pure-Lipid Bilayers and a Mammalian Cell Membrane
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April 2019 |
Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides †
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July 2001 |
Efficient Exploration of Reactive Potential Energy Surfaces Using Car-Parrinello Molecular Dynamics
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June 2003 |
Sampling free energy surfaces as slices by combining umbrella sampling and metadynamics
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April 2016 |
Local elevation: A method for improving the searching properties of molecular dynamics simulation
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December 1994 |
Predicting slow structural transitions in macromolecular systems: Conformational flooding
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September 1995 |
Single-sweep methods for free energy calculations
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May 2008 |
Bridging the gap between thermodynamic integration and umbrella sampling provides a novel analysis method: “Umbrella integration”
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October 2005 |
Variational Approach to Enhanced Sampling and Free Energy Calculations
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August 2014 |
Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint
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May 2016 |
Funnel metadynamics as accurate binding free-energy method
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April 2013 |
On the use of the adiabatic molecular dynamics technique in the calculation of free energy profiles
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March 2002 |
Enhanced sampling in molecular dynamics
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August 2019 |
A Review of Enhanced Sampling Approaches for Accelerated Molecular Dynamics
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January 2016 |
Efficient transition path sampling: Application to Lennard-Jones cluster rearrangements
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June 1998 |
Reaction coordinates of biomolecular isomerization
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May 2000 |
Kinetics of Helix Unfolding: Molecular Dynamics Simulations with Milestoning
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April 2009 |
Full Kinetics of CO Entry, Internal Diffusion, and Exit in Myoglobin from Transition-Path Theory Simulations
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February 2015 |
The Relationship Between Variable Selection and Data Agumentation and a Method for Prediction
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February 1974 |
The perceptron: A probabilistic model for information storage and organization in the brain.
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January 1958 |
Learning representations by back-propagating errors
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October 1986 |
Deep Residual Learning for Image Recognition
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June 2016 |
Backpropagation Applied to Handwritten Zip Code Recognition
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December 1989 |
Gradient Theory of Optimal Flight Paths
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October 1960 |
The numerical solution of variational problems
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August 1962 |
Free energy reconstruction from nonequilibrium single-molecule pulling experiments
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March 2001 |
Free-Energy Landscape for β Hairpin Folding from Combined Parallel Tempering and Metadynamics
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October 2006 |
Locating landmarks on high-dimensional free energy surfaces
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March 2015 |
A self-learning algorithm for biased molecular dynamics
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September 2010 |
Unfolding Hidden Barriers by Active Enhanced Sampling
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July 2018 |
Simplifying the representation of complex free-energy landscapes using sketch-map
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July 2011 |
Using sketch-map coordinates to analyze and bias molecular dynamics simulations
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March 2012 |
Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics
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August 2009 |
A Time-Independent Free Energy Estimator for Metadynamics
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July 2014 |
Iterative Unbiasing of Quasi-Equilibrium Sampling
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November 2019 |
Temperature-Accelerated Sampling and Amplified Collective Motion with Adiabatic Reweighting to Obtain Canonical Distributions and Ensemble Averages
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April 2012 |
THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method
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October 1992 |
Statistically optimal analysis of samples from multiple equilibrium states
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September 2008 |
Optimal Estimation of Free Energies and Stationary Densities from Multiple Biased Simulations
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January 2014 |
Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states
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December 2014 |
Spectral gap optimization of order parameters for sampling complex molecular systems
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February 2016 |
Collective Variables from Local Fluctuations
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May 2018 |
Reweighted autoencoded variational Bayes for enhanced sampling (RAVE)
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August 2018 |
Past–future information bottleneck for sampling molecular reaction coordinate simultaneously with thermodynamics and kinetics
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August 2019 |
Variational Approach to Molecular Kinetics
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March 2014 |
tICA-Metadynamics: Accelerating Metadynamics by Using Kinetically Selected Collective Variables
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May 2017 |
Collective variable discovery and enhanced sampling using autoencoders: Innovations in network architecture and error function design
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August 2018 |
Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction
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June 2006 |
Integrating diffusion maps with umbrella sampling: Application to alanine dipeptide
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April 2011 |
Determination of reaction coordinates via locally scaled diffusion map
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March 2011 |
Predictive collective variable discovery with deep Bayesian models
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January 2019 |
Neural-Network-Based Path Collective Variables for Enhanced Sampling of Phase Transformations
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December 2019 |
LIII. On lines and planes of closest fit to systems of points in space
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November 1901 |
A Global Geometric Framework for Nonlinear Dimensionality Reduction
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December 2000 |
Nonlinear Dimensionality Reduction by Locally Linear Embedding
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December 2000 |
Diffusion maps
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July 2006 |
Nonlinear Dimensionality Reduction
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January 2007 |
Metadynamics in Essential Coordinates: Free Energy Simulation of Conformational Changes
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March 2007 |
t-Distributed Stochastic Neighbor Embedding Method with the Least Information Loss for Macromolecular Simulations
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September 2018 |
Kinetic Pathways of Ion Pair Dissociation in Water
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May 1999 |
T RANSITION P ATH S AMPLING : Throwing Ropes Over Rough Mountain Passes, in the Dark
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October 2002 |
Using Dimensionality Reduction to Systematically Expand Conformational Sampling of Intrinsically Disordered Peptides
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September 2016 |
Probing the Unfolded Configurations of a β-Hairpin Using Sketch-Map
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February 2015 |
EncoderMap: Dimensionality Reduction and Generation of Molecule Conformations
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January 2019 |
Transferable Neural Networks for Enhanced Sampling of Protein Dynamics
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March 2018 |
Separation of a mixture of independent signals using time delayed correlations
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June 1994 |
Slow dynamics in protein fluctuations revealed by time-structure based independent component analysis: The case of domain motions
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February 2011 |
Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9
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March 2013 |
Identification of slow molecular order parameters for Markov model construction
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July 2013 |
Extensible and Scalable Adaptive Sampling on Supercomputers
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November 2020 |
A variational conformational dynamics approach to the selection of collective variables in metadynamics
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November 2017 |
Information Bottleneck Approach to Predictive Inference
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February 2014 |
Diffusion Maps, Reduction Coordinates, and Low Dimensional Representation of Stochastic Systems
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January 2008 |
Principles of maximum entropy and maximum caliber in statistical physics
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July 2013 |
Inferring Transition Rates of Networks from Populations in Continuous-Time Markov Processes
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October 2015 |
Transport, Collective Motion, and Brownian Motion
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March 1965 |
Assessing the Accuracy of Metadynamics †
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April 2005 |
Efficient Reconstruction of Complex Free Energy Landscapes by Multiple Walkers Metadynamics †
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March 2006 |
Free Energy Reconstruction from Metadynamics or Adiabatic Free Energy Dynamics Simulations
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July 2014 |
Random Forests and Adaptive Nearest Neighbors
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June 2006 |
Computing the Free Energy without Collective Variables
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February 2018 |
Gaussian Mixture-Based Enhanced Sampling for Statics and Dynamics
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June 2020 |
Efficient schemes to compute diffusive barrier crossing rates
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April 1997 |
Thermodynamic integration of the free energy along a reaction coordinate in Cartesian coordinates
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May 2000 |
Blue Moon Sampling, Vectorial Reaction Coordinates, and Unbiased Constrained Dynamics
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September 2005 |
Free Energy Surface Reconstruction from Umbrella Samples Using Gaussian Process Regression
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August 2014 |
Multilayer feedforward networks are universal approximators
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January 1989 |
Reinforced dynamics for enhanced sampling in large atomic and molecular systems
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March 2018 |
Comparison of the Performance of Machine Learning Models in Representing High-Dimensional Free Energy Surfaces and Generating Observables
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April 2020 |
Combined Force-Frequency Sampling for Simulation of Systems Having Rugged Free Energy Landscapes
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January 2020 |
Neural networks-based variationally enhanced sampling
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August 2019 |
Adaptive enhanced sampling by force-biasing using neural networks
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April 2018 |
Markov State Models: From an Art to a Science
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February 2018 |
Markov state models of biomolecular conformational dynamics
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April 2014 |
Frequency adaptive metadynamics for the calculation of rare-event kinetics
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August 2018 |
Girsanov reweighting for metadynamics simulations
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August 2018 |
Path probability ratios for Langevin dynamics—Exact and approximate
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March 2021 |
Metadynamics of Paths
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July 2020 |
Markov models of molecular kinetics: Generation and validation
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May 2011 |
EBV noncoding RNA EBER2 interacts with host RNA-binding proteins to regulate viral gene expression
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March 2016 |
Advillin Folding Takes Place on a Hypersurface of Small Dimensionality
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November 2008 |
How Complex Is the Dynamics of Peptide Folding?
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January 2007 |
Estimating the intrinsic dimension of datasets by a minimal neighborhood information
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September 2017 |
Explicit Characterization of the Free-Energy Landscape of a Protein in the Space of All Its Cα Carbons
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December 2019 |
Candidate Binding Sites for Allosteric Inhibition of the SARS-CoV-2 Main Protease from the Analysis of Large-Scale Molecular Dynamics Simulations
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December 2020 |
PLUMED 2: New feathers for an old bird
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February 2014 |
The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask
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August 2014 |
Rethinking Metadynamics: From Bias Potentials to Probability Distributions
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March 2020 |
A Multiscale Coarse-Graining Method for Biomolecular Systems
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February 2005 |
Effective force coarse-graining
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January 2009 |
The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models
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June 2008 |
The relative entropy is fundamental to multiscale and inverse thermodynamic problems
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October 2008 |
Machine Learning of Coarse-Grained Molecular Dynamics Force Fields
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April 2019 |
Ensemble learning of coarse-grained molecular dynamics force fields with a kernel approach
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May 2020 |
Coarse graining molecular dynamics with graph neural networks
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November 2020 |
Deep learning for variational multiscale molecular modeling
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November 2020 |
Multi-body effects in a coarse-grained protein force field
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April 2021 |
Long Time Molecular Dynamics for Enhanced Conformational Sampling in Biomolecular Systems
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October 2004 |
Stochastic, resonance-free multiple time-step algorithm for molecular dynamics with very large time steps
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December 2013 |
Boltzmann generators: Sampling equilibrium states of many-body systems with deep learning
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September 2019 |
Back-mapping based sampling: Coarse grained free energy landscapes as a guideline for atomistic exploration
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October 2019 |