Dice Question Streamline Icon: https://streamlinehq.com

Random seed usage in RGFN’s QuickVina2-GPU docking

Ascertain whether Reaction-GFlowNet (RGFN) used a fixed random seed for QuickVina2-GPU-2.1 docking in the ClpP case study and, if so, identify the seed value and its impact on reproducibility of docking scores and poses.

Information Square Streamline Icon: https://streamlinehq.com

Background

The authors validated their docking protocol by re-docking the reference ligand multiple times with varying random seeds and observed notable differences in docking scores and poses. This variability indicates that seed selection can materially affect results.

Without clarity on whether RGFN set a fixed seed, comparisons may be confounded by stochastic differences in docking outcomes, motivating a need to document the seed configuration used in RGFN’s experiments.

References

When executing QuickVina2-GPU-2.1, if a seed is not specified, a random seed is used. It is unclear if a seed was set in the RGFN work.

— Directly Optimizing for Synthesizability in Generative Molecular Design using Retrosynthesis Models (2407.12186 - Guo et al., 16 Jul 2024) in Appendix, Reproducing RGFN's Oracle — Protocol Validation (Appendix Section; Subsection: Protocol Validation)