Hic Sunt Dracones: Molecular Docking in Uncharted Territories with Structures from AlphaFold2 and RoseTTAfold
- Christian Kersten*
- Steven ClowerSteven ClowerInstitute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128 Mainz, GermanyMore by Steven Clower
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- Fabian BarthelsFabian BarthelsInstitute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128 Mainz, GermanyMore by Fabian Barthels
AlphaFold2 and RoseTTAfold impress with their high accuracy in protein structure prediction. However, for structure-based virtual screenings, not only the overall structure but especially the binding sites need to be accurately predicted. In this work, the docking performance for 66 targets with known ligands but without experimental structures available in the protein data bank was elucidated. The results suggest that using an experimental surrogate–ligand complex is often superior over homology models, and only at low sequence identity to the closest homologue AlphaFold2 structures show an equal performance. The generally high fluctuation of receiver operating characteristic area under the curve values obtained for different homology models suggests that multiple combinations of docking programs and homology models should be tested prior to prospective virtual screenings, and in some cases post-processing of crude models might be necessary.
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This article is cited by 1 publications.
- Ariane Nunes-Alves, Kenneth Merz. AlphaFold2 in Molecular Discovery. Journal of Chemical Information and Modeling 2023, 63
, 5947-5949. https://doi.org/10.1021/acs.jcim.3c01459