ArticleBioorganic & medicinal chemistry2016
Ensemble-based docking: From hit discovery to metabolism and toxicity predictions.
Article in Bioorganic & medicinal chemistry, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 52 citations in OpenAlex.
- Ensemble Docking for Intrinsically Disordered Proteins.Journal of chemical information and modeling · 2025Article
- Ensemble docking for intrinsically disordered proteins.bioRxiv : the preprint server for biology · 2025Article
- Linking machine learning and biophysical structural features in drug discovery.Frontiers in molecular biosciences · 2024Article
- Computational Exploration of Potential CFTR Binding Sites for Type I Corrector Drugs.Biochemistry · 2023Article
- Bioactive Compounds in Garlic (Life (Basel, Switzerland) · 2022Article
- Using Big Data Analytics to "Back Engineer" Protein Conformational Selection Mechanisms.Molecules (Basel, Switzerland) · 2022Article
- Extended-ensemble docking to probe dynamic variation of ligand binding sites during large-scale structural changes of proteins.Chemical science · 2022Article
- Novel Big Data-Driven Machine Learning Models for Drug Discovery Application.Molecules (Basel, Switzerland) · 2022Article
- Big Data analytics for improved prediction of ligand binding and conformational selection.Frontiers in molecular biosciences · 2022Article
- NeuralDock: Rapid and Conformation-Agnostic Docking of Small Molecules.Frontiers in molecular biosciences · 2022Article
- Improving Structure-Based Virtual Screening with Ensemble Docking and Machine Learning.Journal of chemical information and modeling · 2021Article
- Energy penalties enhance flexible receptor docking in a model cavity.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19.Journal of chemical information and modeling · 2020Article
- Structure based virtual screening identifies small molecule effectors for the sialoglycan binding protein Hsa.The Biochemical journal · 2020Article
- Retrospective ensemble docking of allosteric modulators in an adenosine G-protein-coupled receptor.Biochimica et biophysica acta. General subjects · 2020Article
- Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19.ChemRxiv : the preprint server for chemistry · 2020Article
- Targeting the C-Terminal Domain Small Phosphatase 1.Life (Basel, Switzerland) · 2020Review
- Computational Approaches in Preclinical Studies on Drug Discovery and Development.Frontiers in chemistry · 2020Review
- Flavonoids as Putative Epi-Modulators: Insight into Their Binding Mode with BRD4 Bromodomains Using Molecular Docking and Dynamics.Biomolecules · 2018Article
- Ensemble docking to difficult targets in early-stage drug discovery: Methodology and application to fibroblast growth factor 23.Chemical biology & drug design · 2018Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
This paper describes and illustrates the use of ensemble-based docking, i.e., using a collection of protein structures in docking calculations for hit discovery, the exploration of biochemical pathways and toxicity prediction of drug candidates. We describe the computational engineering work necessary to enable large ensemble docking campaigns on supercomputers. We show examples where ensemble-based docking has significantly increased the number and the diversity of validated drug candidates. Finally, we illustrate how ensemble-based docking can be extended beyond hit discovery and toward providing a structural basis for the prediction of metabolism and off-target binding relevant to pre-clinical and clinical trials.
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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.