Related references
Note: Only part of the references are listed.Untitled
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2018)
Self-Guided Langevin Dynamics via Generalized Langevin Equation
Xiongwu Wu et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2016)
Allosteric Effects of Sodium Ion Binding on Activation of the M3 Muscarinic G-Protein-Coupled Receptor
Yinglong Miao et al.
BIOPHYSICAL JOURNAL (2015)
Enhanced sampling techniques in biomolecular simulations
Vojtech Spiwok et al.
BIOTECHNOLOGY ADVANCES (2015)
Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation
Yinglong Miao et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor
Kalli Kappel et al.
QUARTERLY REVIEWS OF BIOPHYSICS (2015)
Direct observation of hierarchical protein dynamics
Jozef R. Lewandowski et al.
SCIENCE (2015)
Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration
Cameron Abrams et al.
ENTROPY (2014)
Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation
Yinglong Miao et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)
Achieving Rigorous Accelerated Conformational Sampling in Explicit Solvent
Urmi Doshi et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2014)
Measuring similarity between dynamic ensembles of biomolecules
Shan Yang et al.
NATURE METHODS (2014)
Free energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamics
Yinglong Miao et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2014)
xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures
Ryan McGreevy et al.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2014)
A Hamiltonian Replica Exchange Molecular Dynamics (MD) Method for the Study of Folding, Based on the Analysis of the Stabilization Determinants of Proteins
Massimiliano Meli et al.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2013)
w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations
Mehrnoosh Arrar et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Population Based Reweighting of Scaled Molecular Dynamics
William Sinko et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2013)
Targeted conformational search with map-restrained self-guided Langevin dynamics: Application to flexible fitting into electron microscopic density maps
Xiongwu Wu et al.
JOURNAL OF STRUCTURAL BIOLOGY (2013)
Activation and dynamic network of the M2 muscarinic receptor
Yinglong Miao et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Coupled Flexibility Change in Cytochrome P450cam Substrate Binding Determined by Neutron Scattering, NMR, and Molecular Dynamics Simulation
Yinglong Miao et al.
BIOPHYSICAL JOURNAL (2012)
Cryo-Electron Microscopy Modeling by the Molecular Dynamics Flexible Fitting Method
Kwok-Yan Chan et al.
BIOPOLYMERS (2012)
Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction
Juuso Lehtivarjo et al.
JOURNAL OF BIOMOLECULAR NMR (2012)
Generalized essential energy space random walks to more effectively accelerate solute sampling in aqueous environment
Chao Lv et al.
JOURNAL OF CHEMICAL PHYSICS (2012)
Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations
William Sinko et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Improved Statistical Sampling and Accuracy with Accelerated Molecular Dynamics on Rotatable Torsions
Urmi Doshi et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics
Levi C. T. Pierce et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Temperature-Dependent Dynamical Transitions of Different Classes of Amino Acid Residue in a Globular Protein
Yinglong Miao et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2012)
Showcasing modern molecular dynamics simulations of membrane proteins through G protein-coupled receptors
Jennifer M. Johnston et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2011)
Accelerating chemical reactions: Exploring reactive free-energy surfaces using accelerated ab initio molecular dynamics
Levi C. T. Pierce et al.
JOURNAL OF CHEMICAL PHYSICS (2011)
Force-momentum-based self-guided Langevin dynamics: A rapid sampling method that approaches the canonical ensemble
Xiongwu Wu et al.
JOURNAL OF CHEMICAL PHYSICS (2011)
Enhanced Lipid Diffusion and Mixing in Accelerated Molecular Dynamics
Yi Wang et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
On the Use of Accelerated Molecular Dynamics to Enhance Configurational Sampling in Ab Initio Simulations
Denis Bucher et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
Adaptive Accelerated Molecular Dynamics (Ad-AMD) Revealing the Molecular Plasticity of P450cam
Phineus R. L. Markwick et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2011)
Studying functional dynamics in bio-molecules using accelerated molecular dynamics
Phineus R. L. Markwick et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2011)
How Fast-Folding Proteins Fold
Kresten Lindorff-Larsen et al.
SCIENCE (2011)
Umbrella sampling
Johannes Kaestner
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2011)
Large-Scale Conformational Changes of Trypanosoma cruzi Proline Racemase Predicted by Accelerated Molecular Dynamics Simulation
Cesar Augusto F. de Oliveira et al.
PLOS COMPUTATIONAL BIOLOGY (2011)
Accessing a Hidden Conformation of the Maltose Binding Protein Using Accelerated Molecular Dynamics
Denis Bucher et al.
PLOS COMPUTATIONAL BIOLOGY (2011)
Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations
Jeff Wereszczynski et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics
Sarah L. Williams et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
Good Practices in Free-Energy Calculations
Andrew Pohorille et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2010)
Adsorption of an Ionic Complementary Peptide on the Hydrophobic Graphite Surface
Yuebiao Sheng et al.
JOURNAL OF PHYSICAL CHEMISTRY C (2010)
Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics
Cameron F. Abrams et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Enhanced conformational sampling of nucleic acids by a new Hamiltonian replica exchange molecular dynamics approach
Jeremy Curuksu et al.
JOURNAL OF CHEMICAL PHYSICS (2009)
Simultaneous escaping of explicit and hidden free energy barriers: Application of the orthogonal space random walk strategy in generalized ensemble based conformational sampling
Lianqing Zheng et al.
JOURNAL OF CHEMICAL PHYSICS (2009)
A computational modeling and molecular dynamics study of the Michaelis complex of human protein Z-dependent protease inhibitor (ZPI) and factor Xa (FXa)
Vasudevan Chandrasekaran et al.
JOURNAL OF MOLECULAR MODELING (2009)
Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics
Barry J. Grant et al.
PLOS COMPUTATIONAL BIOLOGY (2009)
Computational techniques for efficient conformational sampling of proteins
Adam Liwo et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2008)
Thermodynamics and kinetics simulations of multi-time-scale processes for complex systems
Yi Qin Gao et al.
INTERNATIONAL REVIEWS IN PHYSICAL CHEMISTRY (2008)
Essential energy space random walks to accelerate molecular dynamics simulations: Convergence improvements via an adaptive-length self-healing strategy
Lianqing Zheng et al.
JOURNAL OF CHEMICAL PHYSICS (2008)
A statistical analysis of the precision of reweighting-based simulations
Tongye Shen et al.
JOURNAL OF CHEMICAL PHYSICS (2008)
Adaptive biasing force method for scalar and vector free energy calculations
Eric Darve et al.
JOURNAL OF CHEMICAL PHYSICS (2008)
Coupling accelerated molecular dynamics methods with thermodynamic integration simulations
Cesar Augusto F. de Oliveira et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2008)
Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration
Mikolai Fajer et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2008)
Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins
Paul Maragakis et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2008)
E9-Im9 Colicin DNase-Immunity Protein Biomolecular Association in Water: A Multiple-Copy and Accelerated Molecular Dynamics Simulation Study
Riccardo Baron et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2008)
Finding transition pathways using the string method with swarms of trajectories
Albert C. Pan et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2008)
Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems
Lianqing Zheng et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
Alessandro Laio et al.
REPORTS ON PROGRESS IN PHYSICS (2008)
Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics
Leonardo G. Trabuco et al.
STRUCTURE (2008)
Dynamic personalities of proteins
Katherine Henzler-Wildman et al.
NATURE (2007)
Estimating kinetic rates from accelerated molecular dynamics simulations: Alanine dipeptide in explicit solvent as a case study
Cesar Augusto F. De Oliveira et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
Sampling of slow diffusive conformational transitions with accelerated molecular dynamics
Donald Hamelberg et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
Essential energy space random walk via energy space metadynamics method to accelerate molecular dynamics simulations
Hongzhi Li et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
Free-energy landscape for β hairpin folding from combined parallel tempering and metadynamics
Giovanni Bussi et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
String method in collective variables: Minimum free energy paths and isocommittor surfaces
Luca Maragliano et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Free energy landscape and folding mechanism of a β-hairpin in explicit water:: A replica exchange molecular dynamics study
PH Nguyen et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)
Blue moon sampling, vectorial reaction coordinates, and unbiased constrained dynamics
G Ciccotti et al.
CHEMPHYSCHEM (2005)
Molecular dynamics simulations of DNA dimers based on replica-exchange umbrella sampling. I. Test of sampling efficiency
K Murata et al.
JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY (2005)
Application of accelerated molecular dynamics schemes to the production of amorphous silicon
D Choudhary et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine-proline motifs: Accelerated molecular dynamics analysis
D Hamelberg et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)
Free energy calculations for DNA base stacking by replica-exchange umbrella sampling
K Murata et al.
CHEMICAL PHYSICS LETTERS (2004)
Solution conformations of wild-type and mutated Bak BH3 peptides via dynamical conformational sampling and implication to their binding to antiapoptotic Bcl-2 proteins
CY Yang et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2004)
Replica-exchange extensions of simulated tempering method
A Mitsutake et al.
JOURNAL OF CHEMICAL PHYSICS (2004)
Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules
D Hamelberg et al.
JOURNAL OF CHEMICAL PHYSICS (2004)
Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations
Y Okamoto
JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2004)
Self-guided Langevin dynamics simulation method
XW Wu et al.
CHEMICAL PHYSICS LETTERS (2003)
Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurements
J Gore et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
Molecular dynamics of C-peptide of ribonuclease A studied by replica-exchange Monte Carlo method and diffusion theory
G La Penna et al.
CHEMICAL PHYSICS LETTERS (2003)
Understanding folding and design: Replica-exchange simulations of Trp-cage fly miniproteins
JW Pitera et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. I. Formulation and benchmark test
A Mitsutake et al.
JOURNAL OF CHEMICAL PHYSICS (2003)
Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. II. Application to a more complex system
A Mitsutake 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)
Molecular dynamics simulations of biomolecules
M Karplus et al.
NATURE STRUCTURAL BIOLOGY (2002)
Competitive and reversible binding of a guest molecule to its host in aqueous solution through molecular dynamics simulation:: Benzyl alcohol/β-cyclodextrin system
J Varady et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2002)
An adiabatic molecular dynamics method for the calculation of free energy profiles
L Rosso et al.
MOLECULAR SIMULATION (2002)
Calculating free energies using average force
E Darve et al.
JOURNAL OF CHEMICAL PHYSICS (2001)
Ab initio replica-exchange Monte Carlo method for cluster studies
Y Ishikawa et al.
CHEMICAL PHYSICS LETTERS (2001)
Replica-exchange simulated tempering method for simulations of frustrated systems
A Mitsutake et al.
CHEMICAL PHYSICS LETTERS (2000)
Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape
Y Sugita et al.
CHEMICAL PHYSICS LETTERS (2000)
Multidimensional replica-exchange method for free-energy calculations
Y Sugita et al.
JOURNAL OF CHEMICAL PHYSICS (2000)
Targeted molecular dynamics simulations of protein unfolding
P Ferrara et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2000)