ArticleChemical biology & drug design2019
Improving inverse docking target identification with Z-score selection.
Article in Chemical biology & drug design, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Article
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- Computational drug repurposing: approaches, evaluation of in silico resources and case studies.Nature reviews. Drug discovery · 2025Review
- A Computational Approach to Identify Novel Protein Targets Uncovers New Potential Mechanisms of Action of Mirtazapine S(+) and R(-) Enantiomers in Rett Syndrome.Journal of neurochemistry · 2025Article
- Development of Novel Bacterial Topoisomerase Inhibitors Assisted by Computational Screening.ACS medicinal chemistry letters · 2024Article
- Anticancer Activity and Molecular Targets ofBiomedicines · 2023Article
- Targeting Troponin C with Small Molecules Containing Diphenyl Moieties: Calcium Sensitivity Effects on Striated Muscles and Structure-Activity Relationship.Journal of chemical information and modeling · 2023Article
- Identification of four metabolic subtypes and key prognostic markers in lung adenocarcinoma based on glycolytic and glutaminolytic pathways.BMC cancer · 2023Article
- Targeting Troponin C with Small Molecules Containing Diphenyl Moieties: Calcium Sensitivity Effects on Striated Muscle and Structure Activity Relationship.bioRxiv : the preprint server for biology · 2023Article
- Pharmacophore model-aided virtual screening combined with comparative molecular docking and molecular dynamics for identification of marine natural products as SARS-CoV-2 papain-like protease inhibitors.Arabian journal of chemistry · 2022Article
- Complementary Dual Approach for In Silico Target Identification of Potential Pharmaceutical Compounds in Cystic Fibrosis.International journal of molecular sciences · 2022Article
- Target identification for repurposed drugs active against SARS-CoV-2 via high-throughput inverse docking.Journal of computer-aided molecular design · 2022Article
- Identification of Four Metabolic Subtypes of Glioma Based on Glycolysis-Cholesterol Synthesis Genes.Computational and mathematical methods in medicine · 2022Article
- Identification of four gastric cancer subtypes based on genetic analysis of cholesterogenic and glycolytic pathways.Bioengineered · 2021Article
- Identification of Novel Cyclin A2 Binding Site and Nanomolar Inhibitors of Cyclin A2-CDK2 Complex.Current computer-aided drug design · 2021Article
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Authors and funding
3 authors.
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Abstract
The utilization of inverse docking methods for target identification has been driven by an increasing demand for efficient tools for detecting potential drug side-effects. Despite impressive achievements in the field of inverse docking, identifying true positives from a pool of potential targets still remains challenging. Notably, most of the developed techniques have low accuracies, limit the pool of possible targets that can be investigated or are not easy to use for non-experts due to a lack of available scripts or webserver. Guided by our finding that the absolute docking score was a poor indication of a ligand's protein target, we developed a novel "combined Z-score" method that used a weighted fraction of ligand and receptor-based Z-scores to identify the most likely binding target of a ligand. With our combined Z-score method, an additional 14%, 3.6%, and 6.3% of all ligand-protein pairs of the Astex, DUD, and DUD-E databases, respectively, were correctly predicted compared to a docking score-based selection. The combined Z-score had the highest area under the curve in a ROC curve analysis of all three datasets and the enrichment factor for the top 1% predictions using the combined Z-score analysis was the highest for the Astex and DUD-E datasets. Additionally, we developed a user-friendly python script (compatible with both Python2 and Python3) that enables users to employ the combined Z-score analysis for target identification using a user-defined list of ligands and targets. We are providing this python script and a user tutorial as part of the supplemental information.
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