ArticleJournal of chemical information and modeling2020
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19.
Article in Journal of chemical information and modeling, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers.
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91 citing papers in PubMed.
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- Sovereign AI supercomputers: a global landscape review of unprecedented biomedical research infrastructure.Frontiers in artificial intelligence · 2026Review
- A Mini Review on Metal Complexes as Potential Anti-SARS-CoV-2 Agents: Insights from Molecular Docking Studies.Mini reviews in medicinal chemistry · 2026Review
- Gradient Descent to Predict Enzyme Inhibition.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Machine learning for drug-target interaction prediction: A comprehensive review of models, challenges, and computational strategies.Computational and structural biotechnology journal · 2026Review
- Weighted Ensemble Simulations Reveal Novel Conformations and Modulator Effects in Hepatitis B Virus Capsid Assembly.Journal of chemical theory and computation · 2025Article
- Decoding GuaB: Machine Learning-Powered Discovery of Enzyme Inhibitors Against the SuperbugPharmaceuticals (Basel, Switzerland) · 2025Article
- Profiling and cheminformatics bioprospection of curcurbitacin I and momordin Ic fromJournal of enzyme inhibition and medicinal chemistry · 2025Article
- Ultra-large library screening with an evolutionary algorithm in Rosetta (REvoLd).Communications chemistry · 2025Article
- Progress of AI-Driven Drug-Target Interaction Prediction and Lead Optimization.International journal of molecular sciences · 2025Review
- Exploring Novel Inhibitory Compounds Against Phosphatase Gamma 2: A Therapeutic Target for Male Contraceptives.Current issues in molecular biology · 2025Article
- DINC-ensemble: A web server for docking large ligands incrementally to an ensemble of receptor conformations.Journal of molecular biology · 2025Article
- Ultrahigh-Throughput Virtual Screening Strategies against PPI Targets: A Case Study of STAT Inhibitors.Journal of chemical information and modeling · 2025Article
- Structure-Based Design of Small-Molecule Inhibitors of Human Interleukin-6.Molecules (Basel, Switzerland) · 2025Article
- Toward the Prediction of Binding Events in Very Flexible, Allosteric, Multidomain Proteins.Journal of chemical information and modeling · 2025Article
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- Multi-scale computational modeling to identify novel chemical scaffolds as trehalose-6-phosphate phosphatase inhibitors to combatIn silico pharmacology · 2025Article
- Predicting binding events in very flexible, allosteric, multi-domain proteins.bioRxiv : the preprint server for biology · 2024Article
31 more citing papers are in PubMed but not listed here.
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51 authors.
Funding
Abstract
We present a supercomputer-driven pipeline for in silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. Ensemble docking makes use of MD results by docking compound databases into representative protein binding-site conformations, thus taking into account the dynamic properties of the binding sites. We also describe preliminary results obtained for 24 systems involving eight proteins of the proteome of SARS-CoV-2. The MD involves temperature replica exchange enhanced sampling, making use of massively parallel supercomputing to quickly sample the configurational space of protein drug targets. Using the Summit supercomputer at the Oak Ridge National Laboratory, more than 1 ms of enhanced sampling MD can be generated per day. We have ensemble docked repurposing databases to 10 configurations of each of the 24 SARS-CoV-2 systems using AutoDock Vina. Comparison to experiment demonstrates remarkably high hit rates for the top scoring tranches of compounds identified by our ensemble approach. We also demonstrate that, using Autodock-GPU on Summit, it is possible to perform exhaustive docking of one billion compounds in under 24 h. Finally, we discuss preliminary results and planned improvements to the pipeline, including the use of quantum mechanical (QM), machine learning, and artificial intelligence (AI) methods to cluster MD trajectories and rescore docking poses.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.