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Gaussian Accelerated Molecular Dynamics in OpenMM
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Molecular Dynamics Simulations and Kinetic Measurements to Estimate and Predict Protein–Ligand Residence Times
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Molecular Dynamics Simulation for All
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Atomic-Level Characterization of the Structural Dynamics of Proteins
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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
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November 2021
Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation
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SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine
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Equilibrium Sampling in Biomolecular Simulations
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Accuracy of Molecular Simulation-Based Predictions of k off Values: A Metadynamics Study
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Protein–Protein Interaction-Gaussian Accelerated Molecular Dynamics (PPI-GaMD): Characterization of Protein Binding Thermodynamics and Kinetics
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Drug–Target Association Kinetics in Drug Discovery
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Accelerating Rare Dissociative Processes in Biomolecules Using Selectively Scaled MD Simulations
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Binding Kinetics in Drug Discovery
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Drug–Target Interaction Kinetics: Underutilized in Drug Optimization?
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NEW EMBO MEMBER'S REVIEW: Diversity of protein-protein interactions
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Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning
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Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease
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Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration
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Ligand Binding Pathways and Conformational Transitions of the HIV Protease
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Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
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Machine Learning Analysis of τRAMD Trajectories to Decipher Molecular Determinants of Drug-Target Residence Times
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Advances in computational methods for ligand binding kinetics
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ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale
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A High-Throughput Method for Measuring Drug Residence Time Using the Transcreener ADP Assay
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