Unconstrained enhanced sampling for free energy calculations of biomolecules: a review

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(2018)   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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(2016)   JOURNAL OF COMPUTATIONAL CHEMISTRY

Allosteric Effects of Sodium Ion Binding on Activation of the M3 Muscarinic G-Protein-Coupled Receptor

(2015) Yinglong Miao et al.   BIOPHYSICAL JOURNAL

Enhanced sampling techniques in biomolecular simulations

(2015) Vojtech Spiwok et al.   BIOTECHNOLOGY ADVANCES

Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation

(2015) Yinglong Miao et al.   Journal of Chemical Theory and Computation

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(2015)   JOURNAL OF COMPUTATIONAL CHEMISTRY

Self-guided Langevin dynamics via generalized Langevin equation

(2015) Xiongwu Wu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor

(2015) Kalli Kappel et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Direct observation of hierarchical protein dynamics

(2015) J. R. Lewandowski et al.   SCIENCE

Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation

(2014) Yinglong Miao et al.   Journal of Chemical Theory and Computation

Achieving Rigorous Accelerated Conformational Sampling in Explicit Solvent

(2014) Urmi Doshi et al.   Journal of Physical Chemistry Letters

Measuring similarity between dynamic ensembles of biomolecules

(2014) Shan Yang et al.   NATURE METHODS

Free energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamics

(2014) Yinglong Miao et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures

(2014) Ryan McGreevy et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

(2013) Cameron Abrams et al.   Entropy

A Hamiltonian Replica Exchange Molecular Dynamics (MD) Method for the Study of Folding, Based on the Analysis of the Stabilization Determinants of Proteins

(2013) Massimiliano Meli et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Population Based Reweighting of Scaled Molecular Dynamics

(2013) William Sinko et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Targeted conformational search with map-restrained self-guided Langevin dynamics: Application to flexible fitting into electron microscopic density maps

(2013) Xiongwu Wu et al.   JOURNAL OF STRUCTURAL BIOLOGY

Activation and dynamic network of the M2 muscarinic receptor

(2013) Y. Miao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coupled Flexibility Change in Cytochrome P450cam Substrate Binding Determined by Neutron Scattering, NMR, and Molecular Dynamics Simulation

(2012) Yinglong Miao et al.   BIOPHYSICAL JOURNAL

Cryo-Electron Microscopy Modeling by the Molecular Dynamics Flexible Fitting Method

(2012) Kwok-Yan Chan et al.   BIOPOLYMERS

Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction

(2012) Juuso Lehtivarjo et al.   JOURNAL OF BIOMOLECULAR NMR

Generalized essential energy space random walks to more effectively accelerate solute sampling in aqueous environment

(2012) Chao Lv et al.   JOURNAL OF CHEMICAL PHYSICS

Improved Statistical Sampling and Accuracy with Accelerated Molecular Dynamics on Rotatable Torsions

(2012) Urmi Doshi et al.   Journal of Chemical Theory and Computation

Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics

(2012) Levi C.T. Pierce et al.   Journal of Chemical Theory and Computation

w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations

(2012) Mehrnoosh Arrar et al.   Journal of Chemical Theory and Computation

Temperature-Dependent Dynamical Transitions of Different Classes of Amino Acid Residue in a Globular Protein

(2012) Yinglong Miao et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Showcasing modern molecular dynamics simulations of membrane proteins through G protein-coupled receptors

(2011) Jennifer M Johnston et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Accelerating chemical reactions: Exploring reactive free-energy surfaces using acceleratedab initiomolecular dynamics

(2011) Levi C. T. Pierce et al.   JOURNAL OF CHEMICAL PHYSICS

Force-momentum-based self-guided Langevin dynamics: A rapid sampling method that approaches the canonical ensemble

(2011) Xiongwu Wu et al.   JOURNAL OF CHEMICAL PHYSICS

Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations

(2011) William Sinko et al.   Journal of Chemical Theory and Computation

Enhanced Lipid Diffusion and Mixing in Accelerated Molecular Dynamics

(2011) Yi Wang et al.   Journal of Chemical Theory and Computation

On the Use of Accelerated Molecular Dynamics to Enhance Configurational Sampling in Ab Initio Simulations

(2011) Denis Bucher et al.   Journal of Chemical Theory and Computation

Adaptive Accelerated Molecular Dynamics (Ad-AMD) Revealing the Molecular Plasticity of P450cam

(2011) Phineus R. L. Markwick et al.   Journal of Physical Chemistry Letters

Studying functional dynamics in bio-molecules using accelerated molecular dynamics

(2011) Phineus R. L. Markwick et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

Umbrella sampling

(2011) Johannes Kästner   Wiley Interdisciplinary Reviews-Computational Molecular Science

Large-Scale Conformational Changes of Trypanosoma cruzi Proline Racemase Predicted by Accelerated Molecular Dynamics Simulation

(2011) César Augusto F. de Oliveira et al.   PLoS Computational Biology

Accessing a Hidden Conformation of the Maltose Binding Protein Using Accelerated Molecular Dynamics

(2011) Denis Bucher et al.   PLoS Computational Biology

Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations

(2010) Jeff Wereszczynski et al.   Journal of Chemical Theory and Computation

Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics

(2010) Sarah L. Williams et al.   Journal of Chemical Theory and Computation

Good Practices in Free-Energy Calculations

(2010) Andrew Pohorille et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

(2010) C. F. Abrams et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enhanced conformational sampling of nucleic acids by a new Hamiltonian replica exchange molecular dynamics approach

(2009) Jeremy Curuksu et al.   JOURNAL OF CHEMICAL PHYSICS

Simultaneous escaping of explicit and hidden free energy barriers: Application of the orthogonal space random walk strategy in generalized ensemble based conformational sampling

(2009) Lianqing Zheng et al.   JOURNAL OF CHEMICAL PHYSICS

A computational modeling and molecular dynamics study of the Michaelis complex of human protein Z-dependent protease inhibitor (ZPI) and factor Xa (FXa)

(2009) Vasudevan Chandrasekaran et al.   JOURNAL OF MOLECULAR MODELING

Adsorption of an Ionic Complementary Peptide on the Hydrophobic Graphite Surface

(2009) Yuebiao Sheng et al.   Journal of Physical Chemistry C

Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics

(2009) Barry J. Grant et al.   PLoS Computational Biology

Computational techniques for efficient conformational sampling of proteins

(2008) Adam Liwo et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Thermodynamics and kinetics simulations of multi-time-scale processes for complex systems

(2008) Yi Qin Gao et al.   INTERNATIONAL REVIEWS IN PHYSICAL CHEMISTRY

Essential energy space random walks to accelerate molecular dynamics simulations: Convergence improvements via an adaptive-length self-healing strategy

(2008) Lianqing Zheng et al.   JOURNAL OF CHEMICAL PHYSICS

A statistical analysis of the precision of reweighting-based simulations

(2008) Tongye Shen et al.   JOURNAL OF CHEMICAL PHYSICS

Adaptive biasing force method for scalar and vector free energy calculations

(2008) Eric Darve et al.   JOURNAL OF CHEMICAL PHYSICS

Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations

(2008) César Augusto F. de Oliveira et al.   Journal of Chemical Theory and Computation

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

(2008) Mikolai Fajer et al.   Journal of Chemical Theory and Computation

Microsecond Molecular Dynamics Simulation Shows Effect of Slow Loop Dynamics on Backbone Amide Order Parameters of Proteins†

(2008) Paul Maragakis et al.   JOURNAL OF PHYSICAL CHEMISTRY B

E9-Im9 Colicin DNase−Immunity Protein Biomolecular Association in Water: A Multiple-Copy and Accelerated Molecular Dynamics Simulation Study

(2008) Riccardo Baron et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Finding Transition Pathways Using the String Method with Swarms of Trajectories

(2008) Albert C. Pan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems

(2008) L. Zheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

(2008) Alessandro Laio et al.   REPORTS ON PROGRESS IN PHYSICS

Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics

(2008) Leonardo G. Trabuco et al.   STRUCTURE