ArticleMolecular systems biology2022
Benchmarking AlphaFold-enabled molecular docking predictions for antibiotic discovery.
Article in Molecular systems biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 135 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
135 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Antimicrobial resistance crisis: could artificial intelligence be the solution?Military Medical Research · 2024Pooled it
- Article
- A structure-aware generative AI framework for revealing functional relationships in protein families.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Exploring the Potential Neurotoxic Links Between 6PPD/6PPD-Q and Parkinson's Disease Through Network Toxicology and Multi-Dimensional Bioinformatics Analysis.Neurotoxicity research · 2026Article
- Evaluating molecular docking for binding affinity predictions: a systematic analysis of key parameters and the utility of AlphaFold2 structures for the Schrödinger dataset.Journal of computer-aided molecular design · 2026Article
- Deep Contrastive Learning for High-Throughput Prediction of Drug Resistance Mutations from Sequences.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Oxidation-derived metabolites sustain the antioxidant network of quercetin.Journal of computer-aided molecular design · 2026Article
- Bioinformatics identification of candidate biomarkers associated with T cell proliferation in atherosclerosis via WGCNA and machine learning.Journal of cardiothoracic surgery · 2026Article
- Multi-layer network biology combined with single-cell evidence reveals core regulatory nodes in atherosclerotic plaques and potential drug-targeting directions.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
- Gut microbiota-derived metabolites as potential therapeutic agents for intervertebral disc degeneration: insights from network pharmacology and molecular docking.Gut pathogens · 2026Article
- An electron-density point-cloud framework for robust protein-ligand interaction prediction.Nature communications · 2026Article
- The BAHD Acyltransferase Gene Family: Evolutionary Dynamics, Biochemical Mechanisms, and Roles in Plant Stress Adaptation.Plant biotechnology journal · 2026Review
- Prediction of primary human targets and toxicity mechanisms of imidacloprid using integrativeToxicology reports · 2026Article
- Improving AlphaFold2 Performance in Virtual Screens Targeting GPCRs by Enhancing Binding-Site Conformational Sampling.Journal of chemical information and modeling · 2026Article
- Inhibiting NHEJ: In-Silico Approach to Stratifying DNA-PK Inhibitors, Predicting Radio-Halogenation Potential of DNA-PK Inhibitors, and Assessing AlphaFold2 Prediction Accuracy.Bioengineering (Basel, Switzerland) · 2026Article
- In Silico Identification of Dual-Action Compounds Targeting TLR2 andDentistry journal · 2026Article
- Molecular Modeling of the Pathogenetic Mechanisms of Neuropsychiatric Disorders.International journal of molecular sciences · 2026Review
- Integrating metabolomics and machine learning with in silico analysis to identify early biomarkers and molecular interactions in sepsis-associated acute kidney injury.Scientific reports · 2026Article
- Comprehensive identification and validation of hub genes targeted by quercetin in hepatocellular carcinoma via integrated bioinformatics and experimental approaches.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
- Effects of gestational perfluorohexanesulfonic acid exposure at human realistic dose on social communication deficit in mouse offspring.EBioMedicine · 2026Article
75 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
Efficient identification of drug mechanisms of action remains a challenge. Computational docking approaches have been widely used to predict drug binding targets; yet, such approaches depend on existing protein structures, and accurate structural predictions have only recently become available from AlphaFold2. Here, we combine AlphaFold2 with molecular docking simulations to predict protein-ligand interactions between 296 proteins spanning Escherichia coli's essential proteome, and 218 active antibacterial compounds and 100 inactive compounds, respectively, pointing to widespread compound and protein promiscuity. We benchmark model performance by measuring enzymatic activity for 12 essential proteins treated with each antibacterial compound. We confirm extensive promiscuity, but find that the average area under the receiver operating characteristic curve (auROC) is 0.48, indicating weak model performance. We demonstrate that rescoring of docking poses using machine learning-based approaches improves model performance, resulting in average auROCs as large as 0.63, and that ensembles of rescoring functions improve prediction accuracy and the ratio of true-positive rate to false-positive rate. This work indicates that advances in modeling protein-ligand interactions, particularly using machine learning-based approaches, are needed to better harness AlphaFold2 for drug discovery.
Indexed as
Identifiers
What OpenQuestion holds
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.