ArticleProtein science : a publication of the Protein Society2023
Evaluation of AlphaFold2 structures as docking targets.
Article in Protein science : a publication of the Protein Society, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
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- 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
- Target identification and assessment in the era of AI.Nature reviews. Drug discovery · 2026Review
- Unveiling Putative Functions of Burkholderia pseudomallei K96243 Hypothetical Proteins Via High-Throughput Characterization of Structural Similarities.Interdisciplinary sciences, computational life sciences · 2026Article
- Improving AlphaFold2 Performance in Virtual Screens Targeting GPCRs by Enhancing Binding-Site Conformational Sampling.Journal of chemical information and modeling · 2026Article
- Open-Source Molecular Docking and AI-Augmented Structure-Based Drug Design: Current Workflows, Challenges, and Opportunities.International journal of molecular sciences · 2026Review
- Discovery of Covalent Ligands with AlphaFold3.Journal of the American Chemical Society · 2026Article
- Using AlphaFold3 for the Interrogation of Protein Disulfide Bonds.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Computer-aided drug discovery: historical foundations, practical AI tools, and emerging ethical considerations.Frontiers in pharmacology · 2026Review
- Generalizable compound protein interaction prediction with a model incorporating protein structure aware and compound property aware language model representations.Communications chemistry · 2025Article
- Evaluating ligand docking methods for drugging protein-protein interfaces: insights from AlphaFold2 and molecular dynamics refinement.Journal of cheminformatics · 2025Article
- Benchmarking HelixFold3-Predicted Holo Structures for Relative Free Energy Perturbation Calculations.ACS omega · 2025Article
- Proteome-Wide Identification and Comparison of Drug Pockets for Discovering New Drug Indications and Side Effects.Molecules (Basel, Switzerland) · 2025Article
- Developing Generalizable Scoring Functions for Molecular Docking: Challenges and Perspectives.Current medicinal chemistry · 2025Review
- Advances, opportunities, and challenges in methods for interrogating the structure activity relationships of natural products.Natural product reports · 2024Review
- Benchmarking reverse docking through AlphaFold2 human proteome.Protein science : a publication of the Protein Society · 2024Article
- Reliability of AlphaFold2 Models in Virtual Drug Screening: A Focus on Selected Class A GPCRs.International journal of molecular sciences · 2024Article
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Authors and funding
4 authors.
Funding
Abstract
AlphaFold2 is a promising new tool for researchers to predict protein structures and generate high-quality models, with low backbone and global root-mean-square deviation (RMSD) when compared with experimental structures. However, it is unclear if the structures predicted by AlphaFold2 will be valuable targets of docking. To address this question, we redocked ligands in the PDBbind datasets against the experimental co-crystallized receptor structures and against the AlphaFold2 structures using AutoDock-GPU. We find that the quality measure provided during structure prediction is not a good predictor of docking performance, despite accurately reflecting the quality of the alpha carbon alignment with experimental structures. Removing low-confidence regions of the predicted structure and making side chains flexible improves the docking outcomes. Overall, despite high-quality prediction of backbone conformation, fine structural details limit the naive application of AlphaFold2 models as docking targets.
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