Publications by authors named "Agastya P Bhati"

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Rapid, accurate, and reproducible prediction of resistance to antituberculars.
Xibei Zhang, Shunzhou Wan, Agastya P Bhati, Philip W Fowler, Peter V Coveney

mSphere· October 2025

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Equilibrium and Nonequilibrium Ensemble Methods for Accurate, Precise and Reproducible Absolute Binding Free Energy Calculations.
Agastya P Bhati, Shunzhou Wan, Peter V Coveney

J Chem Theory Comput· January 2025

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Optimal Molecular Design: Generative Active Learning Combining REINVENT with Precise Binding Free Energy Ranking Simulations.
Hannes H Loeffler, Shunzhou Wan, Marco Klähn, Agastya P Bhati, Peter V Coveney

J Chem Theory Comput· September 2024

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Comparison of Equilibrium and Nonequilibrium Approaches for Relative Binding Free Energy Predictions.
Shunzhou Wan, Agastya P Bhati, Peter V Coveney

J Chem Theory Comput· November 2023

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Ensemble-Based Approaches Ensure Reliability and Reproducibility.
Shunzhou Wan, Agastya P Bhati, Alexander D Wade, Peter V Coveney

J Chem Inf Model· November 2023

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Long Time Scale Ensemble Methods in Molecular Dynamics: Ligand-Protein Interactions and Allostery in SARS-CoV-2 Targets.
Agastya P Bhati, Art Hoti, Andrew Potterton, Mateusz K Bieniek, Peter V Coveney

J Chem Theory Comput· June 2023

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TIES 2.0: A Dual-Topology Open Source Relative Binding Free Energy Builder with Web Portal.
Mateusz K Bieniek, Alexander D Wade, Agastya P Bhati, Shunzhou Wan, Peter V Coveney

J Chem Inf Model· February 2023

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PLAS-5k: Dataset of Protein-Ligand Affinities from Molecular Dynamics for Machine Learning Applications.
Divya B Korlepara, C S Vasavi, Shruti Jeurkar, Pradeep Kumar Pal, Subhajit Roy, Agastya P Bhati

Sci Data· September 2022

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Alchemical Free Energy Estimators and Molecular Dynamics Engines: Accuracy, Precision, and Reproducibility.
Alexander D Wade, Agastya P Bhati, Shunzhou Wan, Peter V Coveney

J Chem Theory Comput· June 2022

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The performance of ensemble-based free energy protocols in computing binding affinities to ROS1 kinase.
Shunzhou Wan, Agastya P Bhati, David W Wright, Alexander D Wade, Gary Tresadern

Sci Rep· June 2022

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Ensemble Simulations and Experimental Free Energy Distributions: Evaluation and Characterization of Isoxazole Amides as SMYD3 Inhibitors.
Shunzhou Wan, Agastya P Bhati, David W Wright, Ian D Wall, Alan P Graves

J Chem Inf Model· May 2022

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Large Scale Study of Ligand-Protein Relative Binding Free Energy Calculations: Actionable Predictions from Statistically Robust Protocols.
Agastya P Bhati, Peter V Coveney

J Chem Theory Comput· April 2022

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Thermodynamic and structural insights into the repurposing of drugs that bind to SARS-CoV-2 main protease.
Shunzhou Wan, Agastya P Bhati, Alexander D Wade, Dario Alfè, Peter V Coveney

Mol Syst Des Eng· February 2022

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Pattern formation in : An activator-inhibitor model.
Agastya P Bhati, S Goyal, Ram Yadav, Sathyamurthy N

J Biosci· January 2022

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Pandemic drugs at pandemic speed: infrastructure for accelerating COVID-19 drug discovery with hybrid machine learning- and physics-based simulations on high-performance computers.
Agastya P Bhati, Shunzhou Wan, Dario Alfè, Austin R Clyde, Mathis Bode

Interface Focus· December 2021

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TIES 20: Relative Binding Free Energy with a Flexible Superimposition Algorithm and Partial Ring Morphing.
Mateusz K Bieniek, Agastya P Bhati, Shunzhou Wan, Peter V Coveney

J Chem Theory Comput· February 2021

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Rapid, accurate, precise and reproducible ligand-protein binding free energy prediction.
Shunzhou Wan, Agastya P Bhati, Stefan J Zasada, Peter V Coveney

Interface Focus· December 2020

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Ensemble-Based Replica Exchange Alchemical Free Energy Methods: The Effect of Protein Mutations on Inhibitor Binding.
Agastya P Bhati, Shunzhou Wan, Peter V Coveney

J Chem Theory Comput· February 2019

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Uncertainty Quantification in Alchemical Free Energy Methods.
Agastya P Bhati, Shunzhou Wan, Yuan Hu, Brad Sherborne, Peter V Coveney

J Chem Theory Comput· June 2018

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Evaluation and Characterization of Trk Kinase Inhibitors for the Treatment of Pain: Reliable Binding Affinity Predictions from Theory and Computation.
Shunzhou Wan, Agastya P Bhati, Sarah Skerratt, Kiyoyuki Omoto, Veerabahu Shanmugasundaram

J Chem Inf Model· April 2017

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Rapid and Reliable Binding Affinity Prediction of Bromodomain Inhibitors: A Computational Study.
Shunzhou Wan, Agastya P Bhati, Stefan J Zasada, Ian Wall, Darren Green

J Chem Theory Comput· February 2017

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Rapid, Accurate, Precise, and Reliable Relative Free Energy Prediction Using Ensemble Based Thermodynamic Integration.
Agastya P Bhati, Shunzhou Wan, David W Wright, Peter V Coveney

J Chem Theory Comput· January 2017

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