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Exact docking box specification in the RGFN ClpP protocol

Ascertain the precise docking box definition (dimensions and centroid specification) used in the RGFN QuickVina2-GPU-2.1 protocol for the ClpP target, including any parameters or procedures employed to determine box size and position.

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Background

To reproduce the RGFN docking case paper for ClpP, the authors followed the published workflow but encountered ambiguity regarding the docking box specification. They chose a 20 Å × 20 Å × 20 Å box centered at the average coordinates of the reference ligand due to missing details in the RGFN protocol.

Clarifying this implementation detail is necessary for faithful replication and for assessing the comparability of results across different implementations of the docking pipeline.

References

We define the docking box as 20 \AA x 20 \AA x 20 \AA as it was unclear how it should be defined based on RGFN's protocol.

— 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 — Docking Details (Appendix Section; Subsection: Docking Details)