Molecular dynamics simulations of biomolecules
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September 2002 |
Molecular Dynamics Simulation for All
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September 2018 |
Gaussian accelerated molecular dynamics: Principles and applications
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March 2021 |
Dynamic personalities of proteins
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December 2007 |
ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale
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May 2009 |
Showcasing modern molecular dynamics simulations of membrane proteins through G protein-coupled receptors
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August 2011 |
Atomic-Level Characterization of the Structural Dynamics of Proteins
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October 2010 |
To milliseconds and beyond: challenges in the simulation of protein folding
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February 2013 |
Measurement of the millisecond activation switch of G protein–coupled receptors in living cells
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June 2003 |
Viral structural transitions: An all-atom multiscale theory
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December 2006 |
Enhanced sampling techniques in biomolecular simulations
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November 2015 |
Thermodynamics and kinetics simulations of multi-time-scale processes for complex systems
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April 2008 |
Computational techniques for efficient conformational sampling of proteins
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April 2008 |
On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review
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January 2007 |
Unconstrained enhanced sampling for free energy calculations of biomolecules: a review
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July 2016 |
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
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February 1977 |
THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method
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October 1992 |
Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
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journal
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November 2008 |
Using Metadynamics and Path Collective Variables to Study Ligand Binding and Induced Conformational Transitions
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book
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November 2011 |
Adaptive biasing force method for scalar and vector free energy calculations
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journal
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April 2008 |
Calculating Free Energies Using a Scaled-Force Molecular Dynamics Algorithm
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January 2002 |
Steered molecular dynamics investigations of protein function
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February 2001 |
Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations
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May 2004 |
Parallel tempering algorithm for conformational studies of biological molecules
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December 1997 |
Self-guided Langevin dynamics simulation method
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November 2003 |
Self-guided Langevin dynamics via generalized Langevin equation
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July 2015 |
Self-Guided Molecular Dynamics Simulation for Efficient Conformational Search
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August 1998 |
Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules
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June 2004 |
Hyperdynamics: Accelerated Molecular Dynamics of Infrequent Events
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May 1997 |
Sampling of slow diffusive conformational transitions with accelerated molecular dynamics
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October 2007 |
A statistical analysis of the precision of reweighting-based simulations
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July 2008 |
Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation
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May 2014 |
Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation
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July 2015 |
Gaussian Accelerated Molecular Dynamics in NAMD
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December 2016 |
Mechanism of Ligand Recognition by Human ACE2 Receptor
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May 2021 |
Recognition of single-stranded nucleic acids by small-molecule splicing modulators
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July 2021 |
Pathways and Mechanism of Caffeine Binding to Human Adenosine A2A Receptor
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April 2021 |
Pathway and mechanism of drug binding to chemokine receptors revealed by accelerated molecular simulations
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July 2020 |
Mechanisms of γ-Secretase Activation and Substrate Processing
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June 2020 |
Graded activation and free energy landscapes of a muscarinic G-protein–coupled receptor
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October 2016 |
G‐Protein‐Coupled Receptor–Membrane Interactions Depend on the Receptor Activation State
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October 2019 |
Mechanism of the G-protein mimetic nanobody binding to a muscarinic G-protein-coupled receptor
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March 2018 |
Mechanistic Insights into Specific G Protein Interactions with Adenosine Receptors
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July 2019 |
Deciphering Off-Target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics
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March 2019 |
Allosteric Motions of the CRISPR–Cas9 HNH Nuclease Probed by NMR and Molecular Dynamics
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December 2019 |
Replica Exchange Gaussian Accelerated Molecular Dynamics: Improved Enhanced Sampling and Free Energy Calculation
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February 2018 |
Replica-Exchange Umbrella Sampling Combined with Gaussian Accelerated Molecular Dynamics for Free-Energy Calculation of Biomolecules
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journal
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September 2019 |
Ligand Gaussian Accelerated Molecular Dynamics (LiGaMD): Characterization of Ligand Binding Thermodynamics and Kinetics
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July 2020 |
Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy and kinetics calculations of peptide binding
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October 2020 |
Machine Learning for Molecular Simulation
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April 2020 |
Machine learning approaches for analyzing and enhancing molecular dynamics simulations
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April 2020 |
Pharmacogenomics of GPCR Drug Targets
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January 2018 |
Activation of the A2A adenosine G-protein-coupled receptor by conformational selection
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May 2016 |
Activation and allosteric modulation of a muscarinic acetylcholine receptor
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November 2013 |
The Dynamic Process of β2-Adrenergic Receptor Activation
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January 2013 |
Activation mechanism of the 2-adrenergic receptor
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October 2011 |
Activation and dynamic network of the M2 muscarinic receptor
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June 2013 |
Structural insights into differences in G protein activation by family A and family B GPCRs
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July 2020 |
Unique features of different classes of G‐protein‐coupled receptors revealed from sequence coevolutionary and structural analysis
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October 2021 |
GPCR activation mechanisms across classes and macro/microscales
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November 2021 |
Allosteric binding sites on cell-surface receptors: novel targets for drug discovery
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March 2002 |
Allosteric modulators of GPCRs: a novel approach for the treatment of CNS disorders
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January 2009 |
Structural insights into G-protein-coupled receptor allostery
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July 2018 |
Structures of the M1 and M2 muscarinic acetylcholine receptor/G-protein complexes
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May 2019 |
Structure and selectivity engineering of the M 1 muscarinic receptor toxin complex
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July 2020 |
Structural basis for the cooperative allosteric activation of the free fatty acid receptor GPR40
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June 2017 |
Orthosteric and allosteric action of the C5a receptor antagonists
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June 2018 |
Critical Role for the Second Extracellular Loop in the Binding of Both Orthosteric and Allosteric G Protein-coupled Receptor Ligands
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journal
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June 2007 |
The role of the second and third extracellular loops of the adenosine A1 receptor in activation and allosteric modulation
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July 2012 |
Role of the Second Extracellular Loop of the Adenosine A 1 Receptor on Allosteric Modulator Binding, Signaling, and Cooperativity
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journal
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September 2016 |
Structural Basis for Binding of Allosteric Drug Leads in the Adenosine A1 Receptor
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November 2018 |
Extracellular Loop 2 of the Adenosine A 1 Receptor Has a Key Role in Orthosteric Ligand Affinity and Agonist Efficacy
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September 2016 |
A Machine Learning Approach for the Discovery of Ligand-Specific Functional Mechanisms of GPCRs
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June 2019 |
Ligand-Dependent Conformational Transitions in Molecular Dynamics Trajectories of GPCRs Revealed by a New Machine Learning Rare Event Detection Protocol
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May 2021 |
Multi-target dopamine D3 receptor modulators: Actionable knowledge for drug design from molecular dynamics and machine learning
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February 2020 |
Molecular Insights from Conformational Ensembles via Machine Learning
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February 2020 |
A combination of machine learning and infrequent metadynamics to efficiently predict kinetic rates, transition states, and molecular determinants of drug dissociation from G protein-coupled receptors
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September 2020 |
Prediction of Orthosteric and Allosteric Regulations on Cannabinoid Receptors Using Supervised Machine Learning Classifiers
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April 2019 |
Structures of Human A 1 and A 2A Adenosine Receptors with Xanthines Reveal Determinants of Selectivity
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August 2017 |
Structure of the adenosine-bound human adenosine A1 receptor–Gi complex
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June 2018 |
CHARMM36m: an improved force field for folded and intrinsically disordered proteins
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November 2016 |
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald
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August 2013 |
MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories
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October 2015 |
Structure of the Adenosine A1 Receptor Reveals the Basis for Subtype Selectivity
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February 2017 |
The Role of Conformational Ensembles in Ligand Recognition in G-Protein Coupled Receptors
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August 2011 |
Ligand-Dependent Conformations and Dynamics of the Serotonin 5-HT2A Receptor Determine Its Activation and Membrane-Driven Oligomerization Properties
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April 2012 |
Ligand-Dependent Activation and Deactivation of the Human Adenosine A 2A Receptor
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May 2013 |
Ligand-Induced Modulation of the Free-Energy Landscape of G Protein-Coupled Receptors Explored by Adaptive Biasing Techniques
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October 2011 |
Three “hotspots” important for adenosine A2B receptor activation: a mutational analysis of transmembrane domains 4 and 5 and the second extracellular loop
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August 2011 |