AB
Agastya Bhati
Molecular Dynamics Simulationcs.DCcs.CEProteinsDrug Discoveryq-bio.QMAmidesAntitubercular AgentsBacterial Proteinsbinding free energy
On Valency
published · living versionsW_dwz7446r·v1 · currentpublished
FabSim: facilitating computational research through automation on large-scale and distributed e-infrastructures
with Derek Groen, James Suter, James Hetherington, Stefan Zasada +1
1 version
Preprints & journals
32 papers in the corpus · 2015–2026Integrative Physics and Machine Learning-Based Optimal Binding Pose Generator for Protein-Ligand Complexes10.26434/chemrxiv.15009330/v1 · Agastya P Bhati, Jinyu Dong, Sean Black et al.2026 · 0 citationsChemRxiv
Generative Active Learning for Molecular Design with REINVENT: Balancing Binding Affinity and Synthetic Accessibility.42917475 · Klähn, Marco, Loeffler, Hannes H, Wan, Shunzhou et al.2026 · 1 citationJournal of chemical theory and computation. 2026;22(18):9742-9761
IMPECCABLE: A Digital Twin Drug Discovery Workflow Comprising AI, Physics and Experiment & the Creation of Nanomolar-Potent Inhibitors10.26434/chemrxiv.15002535/v3 · Wei Jiang, Agastya P Bhati, Shunzhou Wan et al.2026 · 0 citationsChemRxiv
Generative Active Learning for Molecular Design with REINVENT: Balancing Binding Affinity and Synthetic Accessibility10.26434/chemrxiv.15002493/v2 · Marco Klähn, Hannes H Loeffler, Shunzhou Wan et al.2026 · 1 citationChemRxiv
Rapid, accurate, and reproducible de novo prediction of resistance to antituberculars.40980905 · Zhang, Xibei, Wan, Shunzhou, Bhati, Agastya P et al.2026 · 1 citationmSphere. 2025;10(10):e0057125
Equilibrium and Nonequilibrium Ensemble Methods for Accurate, Precise and Reproducible Absolute Binding Free Energy Calculations.39680850 · Bhati, Agastya P, Wan, Shunzhou, Coveney, Peter V2025 · 14 citationsJournal of chemical theory and computation. 2025;21(1):440-462
Optimal Molecular Design: Generative Active Learning Combining REINVENT with Precise Binding Free Energy Ranking Simulations.39225482 · Loeffler, Hannes H, Wan, Shunzhou, Klähn, Marco et al.2026 · 25 citationsJournal of chemical theory and computation. 2024
Equilibrium and Non-equilibrium Ensemble Methods for Accurate, Precise and Reproducible Absolute Binding Free Energy Calculations10.26434/chemrxiv-2024-sslzp-v3 · Agastya Prakash Bhati, Shunzhou Wan, Peter V. Coveney2024 · 1 citationChemRxiv
Optimal Molecular Design: Generative Active Learning Combining REINVENT with Absolute Binding Free Energy Simulations10.26434/chemrxiv-2024-sr1v6 · Hannes Loeffler, Shunzhou Wan, Marco Klähn et al.2024 · 2 citationsChemRxiv
Ensemble-Based Approaches Ensure Reliability and Reproducibility.37965695 · Wan, Shunzhou, Bhati, Agastya P, Wade, Alexander D et al.2023 · 23 citationsJournal of chemical information and modeling. 2023;63(22):6959-6963
Comparison of Equilibrium and Nonequilibrium Approaches for Relative Binding Free Energy Predictions.37862058 · Wan, Shunzhou, Bhati, Agastya P, Coveney, Peter V2023 · 22 citationsJournal of chemical theory and computation. 2023;19(21):7846-7860
Long Time Scale Ensemble Methods in Molecular Dynamics: Ligand-Protein Interactions and Allostery in SARS-CoV-2 Targets.37246943 · Bhati, Agastya P, Hoti, Art, Potterton, Andrew et al.2023 · 26 citationsJournal of chemical theory and computation. 2023;19(11):3359-3378
TIES 2.0: A Dual-Topology Open Source Relative Binding Free Energy Builder with Web Portal.36719676 · Bieniek, Mateusz K, Wade, Alexander D, Bhati, Agastya P et al.2023 · 3 citationsJournal of chemical information and modeling. 2023;63(3):718-724
PLAS-5k: Dataset of Protein-Ligand Affinities from Molecular Dynamics for Machine Learning Applications.36071074 · Korlepara, Divya B, Vasavi, C S, Jeurkar, Shruti et al.2022 · 28 citationsScientific data. 2022;9(1):548
Which corners to cut? Guidelines on choosing optimal settings to maximise sampling with limited computational resources10.26434/chemrxiv-2022-2jdk2 · Peter V. Coveney, Shunzhou Wan, Agastya P. Bhati et al.2022 · 2 citationsChemRxiv
The performance of ensemble-based free energy protocols in computing binding affinities to ROS1 kinase.35729177 · Wan, Shunzhou, Bhati, Agastya P, Wright, David W et al.2022 · 6 citationsScientific reports. 2022;12(1):10433
Alchemical Free Energy Estimators and Molecular Dynamics Engines: Accuracy, Precision, and Reproducibility.35609233 · Wade, Alexander D, Bhati, Agastya P, Wan, Shunzhou et al.2022 · 36 citationsJournal of chemical theory and computation. 2022;18(6):3972-3987
Ensemble Simulations and Experimental Free Energy Distributions: Evaluation and Characterization of Isoxazole Amides as SMYD3 Inhibitors.35508076 · Wan, Shunzhou, Bhati, Agastya P, Wright, David W et al.2022 · 17 citationsJournal of chemical information and modeling. 2022;62(10):2561-2570
Large Scale Study of Ligand-Protein Relative Binding Free Energy Calculations: Actionable Predictions from Statistically Robust Protocols.35293737 · Bhati, Agastya P, Coveney, Peter V2022 · 33 citationsJournal of chemical theory and computation. 2022;18(4):2687-2702
Thermodynamic and structural insights into the repurposing of drugs that bind to SARS-CoV-2 main protease.35223088 · Wan, Shunzhou, Bhati, Agastya P, Wade, Alexander D et al.2025 · 14 citationsMolecular systems design & engineering. 2022;7(2):123-131
Pandemic Drugs at Pandemic Speed: Infrastructure for Accelerating COVID-19 Drug Discovery with Hybrid Machine Learning- and Physics-based Simulations on High Performance Computers2103.02843v2 · Agastya P. Bhati, Shunzhou Wan, Dario Alfe et al.2021 · 38 citationsInterface Focus. 2021. 11 (6): 20210018
TIES 20: Relative Binding Free Energy with a Flexible Superimposition Algorithm and Partial Ring Morphing.33486956 · Bieniek, Mateusz K, Bhati, Agastya P, Wan, Shunzhou et al.2021 · 25 citationsJournal of chemical theory and computation. 2021;17(2):1250-1265
Pattern formation in Passiflora incarnata: An activator-inhibitor model.34423786 · Bhati, Agastya P, Goyal, S, Yadav, Ram et al.2022 · 5 citationsJournal of biosciences. 2021;46
Scalable HPC and AI Infrastructure for COVID-19 Therapeutics2010.10517v1 · Hyungro Lee, Andre Merzky, Li Tan et al.2020 · 6 citationsarXiv
Rapid, accurate, precise and reproducible ligand-protein binding free energy prediction.33178418 · Wan, Shunzhou, Bhati, Agastya P, Zasada, Stefan J et al.2025 · 153 citationsInterface focus. 2020;10(6):20200007
IMPECCABLE: Integrated Modeling PipelinE for COVID Cure by Assessing Better LEads2010.06574v1 · Aymen Al Saadi, Dario Alfe, Yadu Babuji et al.2020 · 35 citationsarXiv
Ensemble-Based Replica Exchange Alchemical Free Energy Methods: The Effect of Protein Mutations on Inhibitor Binding.30592603 · Bhati, Agastya P, Wan, Shunzhou, Coveney, Peter V2019 · 36 citationsJournal of chemical theory and computation. 2019;15(2):1265-1277
Uncertainty Quantification in Alchemical Free Energy Methods.29678106 · Bhati, Agastya P, Wan, Shunzhou, Hu, Yuan et al.2018 · 70 citationsJournal of chemical theory and computation. 2018;14(6):2867-2880
Evaluation and Characterization of Trk Kinase Inhibitors for the Treatment of Pain: Reliable Binding Affinity Predictions from Theory and Computation.28319380 · Wan, Shunzhou, Bhati, Agastya P, Skerratt, Sarah et al.2017 · 38 citationsJournal of chemical information and modeling. 2017;57(4):897-909
Rapid and Reliable Binding Affinity Prediction of Bromodomain Inhibitors: A Computational Study.28005370 · Wan, Shunzhou, Bhati, Agastya P, Zasada, Stefan J et al.2018 · 77 citationsJournal of chemical theory and computation. 2017;13(2):784-795
Rapid, Accurate, Precise, and Reliable Relative Free Energy Prediction Using Ensemble Based Thermodynamic Integration.27997169 · Bhati, Agastya P, Wan, Shunzhou, Wright, David W et al.2017 · 140 citationsJournal of chemical theory and computation. 2017;13(1):210-222
FabSim: facilitating computational research through automation on large-scale and distributed e-infrastructures1512.02194v1 · Derek Groen, Agastya Bhati, James Suter et al.2015 · 38 citationsarXivon Valency
Career total: 51 works. 32 are in this corpus.
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