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February 2015
Improving the Potential of Mean Force and Nonequilibrium Pulling Simulations by Simultaneous Alchemical Modifications
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Atomic resolution mechanism of ligand binding to a solvent inaccessible cavity in T4 lysozyme
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May 2018
Biomolecular conformational changes and ligand binding: from kinetics to thermodynamics
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Exhaustive Search of Ligand Binding Pathways via Volume-Based Metadynamics
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How Does a Drug Molecule Find Its Target Binding Site?
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Mapping transiently formed and sparsely populated conformations on a complex energy landscape
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Quantitative Characterization of the Binding and Unbinding of Millimolar Drug Fragments with Molecular Dynamics Simulations
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Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models
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Drug–Target Kinetics in Drug Discovery
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Free energy calculation from steered molecular dynamics simulations using Jarzynski’s equality
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Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor
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An Overview of Current Methods to Confirm Protein- Protein Interactions
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Past–future information bottleneck for sampling molecular reaction coordinate simultaneously with thermodynamics and kinetics
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A decade of fragment-based drug design: strategic advances and lessons learned
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The calculation of the potential of mean force using computer simulations
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Relating kinetic rates and local energetic roughness by accelerated molecular-dynamics simulations
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Trends in GPCR drug discovery: new agents, targets and indications
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Mechanisms for Benzene Dissociation through the Excited State of T4 Lysozyme L99A Mutant
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Wepy: A Flexible Software Framework for Simulating Rare Events with Weighted Ensemble Resampling
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Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: Linkage of dynamics and structural plasticity
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Enhanced-Sampling Simulations for the Estimation of Ligand Binding Kinetics: Current Status and Perspective
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Protein Binding Pocket Dynamics
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Implications of protein flexibility for drug discovery
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Binding Analysis Using Accelerated Molecular Dynamics Simulations and Future Perspectives
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Kinetics-Driven Drug Design Strategy for Next-Generation Acetylcholinesterase Inhibitors to Clinical Candidate
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Escape of a Small Molecule from Inside T4 Lysozyme by Multiple Pathways
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March 2018
Delineating Protein–Protein Curvilinear Dissociation Pathways and Energetics with Naïve Multiple‐Walker Umbrella Sampling Simulations
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April 2019
Encounter complexes and hidden poses of kinase-inhibitor binding on the free-energy landscape
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August 2019
Standard Free Energy of Binding from a One-Dimensional Potential of Mean Force
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March 2009
Development and testing of a general amber force field
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January 2004
Molecular dynamics simulations of biomolecules
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September 2002
Protein–protein binding pathways and calculations of rate constants using fully-continuous, explicit-solvent simulations
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January 2019
Insulin Dissociates by Diverse Mechanisms of Coupled Unfolding and Unbinding
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June 2020
Unbinding Kinetics of a p38 MAP Kinase Type II Inhibitor from Metadynamics Simulations
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March 2017
Estimation of Drug-Target Residence Times by τ-Random Acceleration Molecular Dynamics Simulations
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May 2018
Boron Mimetics: 1,2-Dihydro-1,2-azaborines Bind inside a Nonpolar Cavity of T4 Lysozyme
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September 2009
Toward Achieving Efficient and Accurate Ligand-Protein Unbinding with Deep Learning and Molecular Dynamics through RAVE
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November 2018
Recent progress in molecular simulation methods for drug binding kinetics
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October 2020
Replica-exchange molecular dynamics method for protein folding
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Predicting Residence Time and Drug Unbinding Pathway through Scaled Molecular Dynamics
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Kinetics for Drug Discovery: an industry-driven effort to target drug residence time
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June 2017
Ligand Gaussian Accelerated Molecular Dynamics (LiGaMD): Characterization of Ligand Binding Thermodynamics and Kinetics
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Dynamical control by water at a molecular level in protein dimer association and dissociation
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Chromophore Channeling in the G-Protein Coupled Receptor Rhodopsin
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PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
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June 2013
Anton 3
Shaw, David E.; Adams, Peter J.; Azaria, Asaph
Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis
https://doi.org/10.1145/3458817.3487397
conference
November 2021
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
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July 2015
Ligand unbinding mechanisms and kinetics for T4 lysozyme mutants from τRAMD simulations
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January 2021
Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation
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May 2014
Ab Initio prediction of protein–ligand binding structures by replica‐exchange umbrella sampling simulations
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June 2011
REVO: Resampling of ensembles by variation optimization
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June 2019
Cryo-EM in drug discovery: achievements, limitations and prospects
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Efficient Refinement and Free Energy Scoring of Predicted Protein–Protein Complexes Using Replica Exchange with Repulsive Scaling
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October 2020
Frequency adaptive metadynamics for the calculation of rare-event kinetics
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Acceleration of biomolecular kinetics in Gaussian accelerated molecular dynamics
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August 2018
The Use of Thermodynamic and Kinetic Data in Drug Discovery: Decisive Insight or Increasing the Puzzlement?
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December 2014
Advances in free-energy-based simulations of protein folding and ligand binding
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February 2016
Protein–Protein Interaction-Gaussian Accelerated Molecular Dynamics (PPI-GaMD): Characterization of Protein Binding Thermodynamics and Kinetics
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January 2022
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
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October 2003
Applying thermodynamic profiling in lead finding and optimization
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Drug–Target Association Kinetics in Drug Discovery
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October 2019
De Novo Prediction of Binders and Nonbinders for T4 Lysozyme by gREST Simulations
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August 2019
Accelerating Rare Dissociative Processes in Biomolecules Using Selectively Scaled MD Simulations
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September 2019
Dynamics, Hydration, and Motional Averaging of a Loop-Gated Artificial Protein Cavity: The W191G Mutant of Cytochrome c Peroxidase in Water as Revealed by Molecular Dynamics Simulations
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August 2007
Access of ligands to cavities within the core of a protein is rapid
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June 1996
Extracting Realistic Kinetics of Rare Activated Processes from Accelerated Molecular Dynamics Using Kramers’ Theory
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January 2011
Reaction Coordinate-Free Approach to Recovering Kinetics from Potential-Scaled Simulations: Application of Kramers’ Rate Theory
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June 2016
Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation
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July 2015
Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy and kinetics calculations of peptide binding
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October 2020
Binding Kinetics in Drug Discovery
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VMD: Visual molecular dynamics
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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
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NEW EMBO MEMBER'S REVIEW: Diversity of protein-protein interactions
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Efficient Determination of Protein–Protein Standard Binding Free Energies from First Principles
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Protein conformational flexibility modulates kinetics and thermodynamics of drug binding
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Blind Prediction of Charged Ligand Binding Affinities in a Model Binding Site
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Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration
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Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect
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Molecular Basis of Ligand Dissociation in β-Adrenergic Receptors
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CHARMM additive and polarizable force fields for biophysics and computer-aided drug design
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Molecular determinants of drug–receptor binding kinetics
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A cavity-containing mutant of T4 lysozyme is stabilized by buried benzene
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Binding Thermodynamics and Kinetics Calculations Using Chemical Host and Guest: A Comprehensive Picture of Molecular Recognition
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On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities
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January 2012
Generation of ligand binding sites in T4 lysozyme by deficiency-creating substitutions
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Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules
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June 2004
Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
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Internal dynamics of proteins. Short time and long time motions of aromatic sidechains in PTI
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Kinetics of protein–ligand unbinding: Predicting pathways, rates, and rate-limiting steps
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Unconstrained enhanced sampling for free energy calculations of biomolecules: a review
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Efficient Characterization of Protein Cavities within Molecular Simulation Trajectories: trj_cavity
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Pathway and mechanism of drug binding to G-protein-coupled receptors
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Ranking protein–protein docking results using steered molecular dynamics and potential of mean force calculations
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Finding multiple reaction pathways of ligand unbinding
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