RT Journal Article
SR Electronic
T1 A resource for comparing AF-Cluster and other AlphaFold2 sampling methods
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2024.07.29.605333
DO 10.1101/2024.07.29.605333
A1 Wayment-Steele, Hannah K.
A1 Ovchinnikov, Sergey
A1 Colwell, Lucy
A1 Kern, Dorothee
YR 2024
UL http://biorxiv.org/content/early/2024/07/30/2024.07.29.605333.abstract
AB We are excited that Porter et al. have explored [1-3] the AF-Cluster [4] algorithm – this is critical for the field to advance. Increasingly many methods have been reported for perturbing and sampling AlphaFold2 (AF2) [5]. If multiple methods achieve similar results, that does not in itself invalidate any method, nor does it answer why these methods work. To help the field continue to try to answer these questions, we wish to highlight a few discrepancies between the AF-Cluster method as presented originally in our work [4] and the subsequent discussion in refs. [1-3]. We hope that this short work clarifies potential misunderstandings.Competing Interest StatementD.K. is a co-founder of Relay Therapeutics and MOMA Therapeutics. The remaining authors declare no competing interests.