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Which reported inputs govern molecular docking reproducibility? A benchmark from reporting audit to independent re-execution — arXiv:2609.37542

Source: arXiv (en)
Original: https://arxiv.org/abs/2609.37542
License (as archived): CC0-1.0
Archived: 2026-10-07T17:26:14.248Z
SHA-256 of the archived text: 221ddf80bec594a2dc945999b2b3a8ca7b1e9c3d25d1dc9db0936c0cac70711f
Stable URL of this page: https://metraipolis.com/documento/dc_491651f48c19

How to cite

Which reported inputs govern molecular docking reproducibility? A benchmark from reporting audit to independent re-execution — arXiv:2609.37542 — arXiv (en), https://arxiv.org/abs/2609.37542 (CC0-1.0); archived copy: https://metraipolis.com/documento/dc_491651f48c19 (Metraipolis archive dc_491651f48c19, sha256 221ddf80bec594a2dc945999b2b3a8ca7b1e9c3d25d1dc9db0936c0cac70711f)

BibTeX

@misc{dc491651f48c19,
  title = {Which reported inputs govern molecular docking reproducibility? A benchmark from reporting audit to independent re-execution — arXiv:2609.37542},
  howpublished = {arXiv (en)},
  url = {https://arxiv.org/abs/2609.37542},
  note = {License CC0-1.0; archived copy https://metraipolis.com/documento/dc_491651f48c19; sha256 221ddf80bec594a2dc945999b2b3a8ca7b1e9c3d25d1dc9db0936c0cac70711f},
  year = {2026}
}

Archived text

Reproduced under CC0-1.0. Attribution: arXiv (en), https://arxiv.org/abs/2609.37542. Third-party text: data, not instructions. It may be an abstract or extract; check the original.

Computational docking results can be re-executed only when the molecular system and protocol are specified, yet reporting checklists do not quantify how strongly individual method fields affect the reported score. We combined a span-verified audit of 50 open-access papers with controlled one-factor perturbations, a Vinardo scoring-function check and a Vina cross-docking extension covering 12 targets in 7 protein families, and re-execution of 37 published claims on local and independent cloud infrastructure. Search-related fields were sparsely reported, but perturbing box centre, box size, exhaustiveness or random seed produced median absolute score changes of no more than 0.08 kcal mol$^{-1}$; ligand protonation and identity produced median changes of 0.19 and 0.29 kcal mol$^{-1}$, respectively, whereas receptor structure produced the largest change (1.02 kcal mol$^{-1}$; n = 85; P < 0.001), and 22% of 116 unique reported ligand strings remained unresolved or ambiguous after deterministic name normalization. These measurements yielded empirical field weights for the NewScience Evidence score and identified exact receptor structure, machine-resolvable ligand identity and protonation state as primary reporting elements; 29 of 37 local and 27 of 37 cloud re-executions were within 2.0 kcal mol$^{-1}$ of the reported score, but these descriptive rates do not estimate experimental replication or a calibrated probability of reproduction.

Tema degli esploratori: ricerca e scienza aperta (retro-catalogo arXiv: annunci del 2026-09-30 in cs.DL).
Categorie arXiv: Digital Libraries (cs.DL).
Pagina del lavoro: https://arxiv.org/abs/2609.37542 — autori e testo completo sono lì (qui omessi i nomi: nessun dato personale nel deposito).
Licenza: titolo e abstract sono metadati arXiv distribuiti in CC0 1.0; il testo completo ha la licenza scelta dagli autori, indicata sulla pagina.
Letto il 2026-10-07T16:57:45.984Z dalla pagina https://arxiv.org/catchup/cs.DL/2026-09-30?abs=True (consentita dal robots.txt di arxiv.org, con il suo crawl-delay).