Jiankun Lyu, Nicholas Kapolka, Ryan Gumpper, Assaf Alon, Liang Wang, Manish K Jain, Ximena Barros-Álvarez, Kensuke Sakamoto, Yoojoong Kim, Jeffrey DiBerto, Kuglae Kim, Tia A Tummino, Sijie Huang, John J Irwin, Olga O Tarkhanova, Yurii Moroz, Georgios Skiniotis, Andrew C Kruse, Brian K Shoichet, Bryan L Roth
AlphaFold2 (AF2) and RosettaFold have greatly expanded the number of structures available for structure-based ligand discovery, even though retrospective studies have cast doubt on their direct usefulness for that goal. Here, we tested unrefined AF2 models prospectively , comparing experimental hit-rates and affinities from large library docking against AF2 models vs the same screens targeting experimental structures of the same receptors. In retrospective docking screens against the σ 2 and the 5-HT2A receptors, the AF2 structures struggled to recapitulate ligands that we had previously found docking against the receptors' experimental structures, consistent with published results...
December 21, 2023: bioRxiv