相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。Membrane-Mediated Ligand Unbinding of the PK-11195 Ligand from TSPO
Tom Dixon et al.
BIOPHYSICAL JOURNAL (2021)
Structural Mechanism of ω-Currents in a Mutated Kv7.2 Voltage Sensor Domain from Molecular Dynamics Simulations
Giulio Alberini et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2021)
A Minimal, Adaptive Binning Scheme for Weighted Ensemble Simulations
Paul A. Torrillo et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2021)
The RED scheme: Rate-constant estimation from pre-steady state weighted ensemble simulations
Alex J. DeGrave et al.
JOURNAL OF CHEMICAL PHYSICS (2021)
Catalytic Magnesium as a Door Stop for DNA Sliding
Hao Wang et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2021)
Computer Simulations of the Dissociation Mechanism of Gleevec from Abl Kinase with Milestoning
Brajesh Narayan et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2021)
Free energy and kinetics of cAMP permeation through connexin26 via applied voltage and milestoning
Wenjuan Jiang et al.
BIOPHYSICAL JOURNAL (2021)
ScMile: A Script to Investigate Kinetics with Short Time Molecular Dynamics Trajectories and the Milestoning Theory
Wei Wei et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)
Transient States and Barriers from Molecular Simulations and the Milestoning Theory: Kinetics in Ligand-Protein Recognition and Compound Design
Zhiye Tang et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)
The transition between active and inactive conformations of Abl kinase studied by rock climbing and Milestoning
Brajesh Narayan et al.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS (2020)
Finding an Optimal Pathway on a Multidimensional Free-Energy Landscape
Haohao Fu et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)
Milestoning with wind: Exploring the impact of a biasing potential in exact calculation of kinetics
Hao Wang et al.
JOURNAL OF CHEMICAL PHYSICS (2020)
Weighted ensemble milestoning (WEM): A combined approach for rare event simulations
Dhiman Ray et al.
JOURNAL OF CHEMICAL PHYSICS (2020)
Predicting Ligand Binding Kinetics Using a Markovian Milestoning with Voronoi Tessellations Multiscale Approach
Benjamin R. Jagger et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)
On Calculating Free Energy Differences Using Ensembles of Transition Paths
Robert Hall et al.
FRONTIERS IN MOLECULAR BIOSCIENCES (2020)
Free Energy Landscape and Conformational Kinetics of Hoogsteen Base Pairing in DNA vs. RNA
Dhiman Ray et al.
BIOPHYSICAL JOURNAL (2020)
Multisecond ligand dissociation dynamics from atomistic simulations
Steffen Wolf et al.
NATURE COMMUNICATIONS (2020)
Thermodynamics and Kinetics of Ion Permeation in Wild-Type and Mutated Open Active Conformation of the Human α7 Nicotinic Receptor
Grazia Cottone et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)
Kinetics and free energy of ligand dissociation using weighted ensemble milestoning
Dhiman Ray et al.
JOURNAL OF CHEMICAL PHYSICS (2020)
Accelerated Estimation of Long-Timescale Kinetics from Weighted Ensemble Simulation via Non-Markovian Microbin Analysis
Jeremy Copperman et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)
Committors, first-passage times, fluxes, Markov states, milestones, and all that
Alexander M. Berezhkovskii et al.
JOURNAL OF CHEMICAL PHYSICS (2019)
Computational Estimation of Microsecond to Second Atomistic Folding Times
Upendra Adhikari et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2019)
REVO: Resampling of ensembles by variation optimization
Nazanin Donyapour et al.
JOURNAL OF CHEMICAL PHYSICS (2019)
Taming Rugged Free Energy Landscapes Using an Average Force
Haohao Fu et al.
ACCOUNTS OF CHEMICAL RESEARCH (2019)
Accelerating the Calculation of Protein-Ligand Binding Free Energy and Residence Times Using Dynamically Optimized Collective Variables
Z. Faidon Brotzakis et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)
Ion Permeation through a Phospholipid Membrane: Transition State, Path Splitting, and Calculation of Permeability
Arman Fathizadeh et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)
Protein-protein binding pathways and calculations of rate constants using fully-continuous, explicit-solvent simulations
Ali S. Saglam et al.
CHEMICAL SCIENCE (2019)
Unbiased Molecular Dynamics of 11 min Timescale Drug Unbinding Reveals Transition State Stabilizing Interactions
Samuel D. Lotz et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2018)
Advances in milestoning. I. Enhanced sampling via wind-assisted reweighted milestoning (WARM)
Gianmarc Grazioli et al.
JOURNAL OF CHEMICAL PHYSICS (2018)
Zooming across the Free-Energy Landscape: Shaving Barriers, and Flooding Valleys
Haohao Fu et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2018)
Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach
Benjamin R. Jagger et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2018)
Targeted Molecular Dynamics Calculations of Free Energy Profiles Using a Nonequilibrium Friction Correction
Steffen Wolf et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)
Molecular Dynamics Simulations of Ion Selectivity in a Claudin-15 Paracellular Channel
Giulio Alberini et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2018)
Probing Translocation in Mutants of the Anthrax Channel: Atomically Detailed Simulations with Milestoning
Piao Ma et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2018)
Trajectory Stratification of Stochastic Dynamics
Aaron R. Dinner et al.
SIAM REVIEW (2018)
Calculating Iso-Committor Surfaces as Optimal Reaction Coordinates with Milestoning
Ron Elber et al.
ENTROPY (2017)
Free Energy Coupling between DNA. Bending and Base Flipping
Ning Ma et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2017)
Quantitative Characterization of the Binding and Unbinding of Millimolar Drug Fragments with Molecular Dynamics Simulations
Albert C. Pan et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2017)
SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding
Lane W. Votapka et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2017)
The Impact of Protonation on Early Translocation of Anthrax Lethal Factor: Kinetics from Molecular Dynamics Simulations and Milestoning Theory
Piao Ma et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2017)
Path-sampling strategies for simulating rare events in biomolecular systems
Lillian T. Chong et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2017)
Multiple Ligand Unbinding Pathways and Ligand-Induced Destabilization Revealed by WExplore
Alex Dickson et al.
BIOPHYSICAL JOURNAL (2017)
Adaptive Multilevel Splitting Method for Molecular Dynamics Calculation of Benzamidine-Trypsin Dissociation Time
Ivan Teo et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)
Accurate Estimation of Protein Folding and Unfolding Times: Beyond Markov State Models
Ernesto Suarez et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)
Markovian and Non-Markovian Modeling of Membrane Dynamics with Milestoning
Alfredo E. Cardenas et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2016)
Ligand Release Pathways Obtained with WExplore: Residence Times and Mechanisms
Alex Dickson et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2016)
Two Relations to Estimate Membrane Permeability Using Milestoning
Lane W. Votapka et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2016)
Efficient Atomistic Simulation of Pathways and Calculation of Rate Constants for a Protein-Peptide Binding Process: Application to the MDM2 Protein and an Intrinsically Disordered p53 Peptide
Matthew C. Zwier et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2016)
Tabulation as a high-resolution alternative to coarse-graining protein interactions: Initial application to virus capsid subunits
Justin Spiriti et al.
JOURNAL OF CHEMICAL PHYSICS (2015)
Exact milestoning
Juan M. Bello-Rivas et al.
JOURNAL OF CHEMICAL PHYSICS (2015)
Simulating Current-Voltage Relationships for a Narrow Ion Channel Using the Weighted Ensemble Method
Joshua L. Adelman et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
WESTPA: An Interoperable, Highly Scalable Software Package for Weighted Ensemble Simulation and Analysis
Matthew C. Zwier et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
James A. Maier et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
Full Kinetics of CO Entry, Internal Diffusion, and Exit in Myoglobin from Transition-Path Theory Simulations
Tang-Qing Yu et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2015)
Mechanism of Substrate Trans location by a Ring-Shaped ATPase Motor at Millisecond Resolution
Wen Ma et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2015)
Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field
Lingle Wang et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2015)
Kinetics of protein-ligand unbinding: Predicting pathways, rates, and rate-limiting steps
Pratyush Tiwary et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)
Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models
Nuria Plattner et al.
NATURE COMMUNICATIONS (2015)
Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning
Lane W. Votapka et al.
PLOS COMPUTATIONAL BIOLOGY (2015)
AWE-WQ: Fast-Forwarding Molecular Dynamics Using the Accelerated Weighted Ensemble
Badi' Abdul-Wahid et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2014)
Simultaneous Computation of Dynamical and Equilibrium Information Using a Weighted Ensemble of Trajectories
Ernesto Suarez et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)
WExplore: Hierarchical Exploration of High-Dimensional Spaces Using the Weighted Ensemble Algorithm
Alex Dickson et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2014)
CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data
Jing Huang et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2013)
Using collective variables to drive molecular dynamics simulations
Giacomo Fiorin et al.
MOLECULAR PHYSICS (2013)
Functional efficacy of adenosine A2A receptor agonists is positively correlated to their receptor residence time
Dong Guo et al.
BRITISH JOURNAL OF PHARMACOLOGY (2012)
Steered transition path sampling
Nicholas Guttenberg et al.
JOURNAL OF CHEMICAL PHYSICS (2012)
Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition
Jeff Wereszczynski et al.
QUARTERLY REVIEWS OF BIOPHYSICS (2012)
Efficient Explicit-Solvent Molecular Dynamics Simulations of Molecular Association Kinetics: Methane/Methane, Na+/Cl-, Methane/Benzene, and K+/18-Crown-6 Ether
Matthew C. Zwier et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
Ignasi Buch et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
The weighted ensemble path sampling method is statistically exact for a broad class of stochastic processes and binning procedures
Bin W. Zhang et al.
JOURNAL OF CHEMICAL PHYSICS (2010)
Milestoning without a Reaction Coordinate
Peter Majek et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
Markovian milestoning with Voronoi tessellations
Eric Vanden-Eijnden et al.
JOURNAL OF CHEMICAL PHYSICS (2009)
Free Energy and Kinetics of Conformational Transitions from Voronoi Tessellated Milestoning with Restraining Potentials
Luca Maragliano et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)
Probability distributions of molecular observables computed from Markov models
Frank Noe
JOURNAL OF CHEMICAL PHYSICS (2008)
On the assumptions underlying milestoning
Eric Vanden-Eijnden et al.
JOURNAL OF CHEMICAL PHYSICS (2008)
Exact low-force kinetics from high-force single-molecule unfolding events
Jeremiah Nummela et al.
BIOPHYSICAL JOURNAL (2007)
A milestoning study of the kinetics of an allosteric transition:: Atomically detailed simulations of deoxy Scapharca hemoglobin
Ron Elber
BIOPHYSICAL JOURNAL (2007)
Extending molecular dynamics time scales with milestoning: Example of complex kinetics in a solvated peptide
Anthony M. A. West et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
Opinion - Drug-target residence time and its implications for lead optimization
Robert A. Copeland et al.
NATURE REVIEWS DRUG DISCOVERY (2006)
On the calculation of time correlation functions by potential scaling
CY Xing et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Scalable molecular dynamics with NAMD
JC Phillips et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)
Development and testing of a general amber force field
JM Wang et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
Computing time scales from reaction coordinates by milestoning
AK Faradjian et al.
JOURNAL OF CHEMICAL PHYSICS (2004)
Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew
HW Horn et al.
JOURNAL OF CHEMICAL PHYSICS (2004)
A novel path sampling method for the calculation of rate constants
TS van Erp et al.
JOURNAL OF CHEMICAL PHYSICS (2003)
Escaping free-energy minima
A Laio et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
Calculating free energies using average force
E Darve et al.
JOURNAL OF CHEMICAL PHYSICS (2001)