A resource for comparing AF-Cluster and other AlphaFold2 sampling methods

Abstract

AbstractWe 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 answerwhythese 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.