ArticleACS omega2022
Systematic Investigation of Docking Failures in Large-Scale Structure-Based Virtual Screening.
Article in ACS omega, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Efficacy of tannins as silage additives to inhibit deamination process during ensiling: a meta-analysis andVeterinary and animal science · 2026Article
- Docking-based virtual screening: Past, present, and future.Biophysical journal · 2026Review
- Pyridine electrooxidation on polycrystalline platinum: a combined computational and electrochemical mechanistic study.Journal of molecular modeling · 2026Article
- MOZAIC: compound growth via in silico reactions and global optimization using Conformational Space Annealing.Bioinformatics (Oxford, England) · 2026Article
- Computational investigation for exploring botanical ingredients as potential negative allosteric modulators targeting metabotropic glutamate receptor 5.Research in pharmaceutical sciences · 2026Article
- 1,5-Disubstituted Tetrazoles as Promising Anticancer Resistance Agents: A Chemoinformatic Characterization.ACS omega · 2026Article
- Reproducibility, validation, and failure modes across classical and AI-driven molecular docking.Journal of computer-aided molecular design · 2026Review
- Nature meets machine: the AI renaissance in natural product drug discovery.Natural products and bioprospecting · 2026Review
- Robustness Analyses Substantially Narrow in silico Network-Toxicology Signals Linking Selected Pharmaceuticals and Caffeine to Vitiligo.Clinical, cosmetic and investigational dermatology · 2026Article
- Role of tannin, saponin, and cumin in inhibiting deamination during ensiling: A molecular docking and molecular dynamics approach.Open veterinary journal · 2025Article
- Assay2Mol: Large Language Model-based Drug Design Using BioAssay Context.Proceedings of the Conference on Empirical Methods in Natural Language Processing. Conference on Empirical Methods in Natural Language Processing · 2025Article
- Article
- Integrated bioinformatics analysis identifies CHAD association with osteoporosis and in vitro chondrogenic effects of Wogonin.Scientific reports · 2025Article
- Molecular Docking in Drug Discovery: Techniques, Applications, and Advancements.Current medicinal chemistry · 2025Review
- Accelerating drug discovery and repurposing by combining transcriptional signature connectivity with docking.Science advances · 2024Article
- Building shape-focused pharmacophore models for effective docking screening.Journal of cheminformatics · 2024Article
- Benchmarking different docking protocols for predicting the binding poses of ligands complexed with cyclooxygenase enzymes and screening chemical libraries.BioImpacts : BI · 2024Article
- Article
- Considerations Around Structure-Based Drug Discovery for KRAS Using DOCK.Methods in molecular biology (Clifton, N.J.) · 2024Article
- AiKPro: deep learning model for kinome-wide bioactivity profiling using structure-based sequence alignments and molecular 3D conformer ensemble descriptors.Scientific reports · 2023Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In recent years, large-scale structure-based virtual screening has attracted increasing levels of interest for identification of novel compounds corresponding to potential drug targets. It is critical to understand the strengths and weaknesses of docking algorithms to increase the success rate in practical applications. Here, we systematically investigated the docking successes and failures of two representative docking programs: UCSF DOCK 3.7 and AutoDock Vina. DOCK 3.7 performed better in early enrichment on the Directory of Useful Decoys: Enhanced (DUD-E) data set, although both docking methods were roughly comparable in overall enrichment performance. DOCK 3.7 also showed superior computational efficiency. Intriguingly, the Vina scoring function showed a bias toward compounds with higher molecular weights. Both the tested docking approaches yielded incorrectly predicted ligand binding poses caused by the limitations of torsion sampling. Based on a careful analysis of docking results from six representative cases, we propose the reasons underlying docking failures; furthermore, we provide a few solutions, representing practical guidance for large-scale virtual screening campaigns and future docking algorithm development.
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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.