biostudies-literatureHolcomb MNational Institute of General Medical Sciencese4530https://www.ebi.ac.uk/biostudies/studies/S-EPMC9794023biostudies-literatureUnknown32(1)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 makiProtein science : a publication of the Protein SocietyEvaluation of AlphaFold2 structures as docking targets.PMC9794023GM069832Goodsell DSHolcomb MChang YTForli SfalseEvaluation of AlphaFold2 structures as docking targets.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 maki2023-01-01T00:00:00Z2023 Jan2025-04-22T10:09:49.091Z2025-04-05T23:30:06.671ZS-EPMC97940233647977610.1002/pro.4530