Measuring the Re-executability of Published Molecular Docking Claims

Abstract

Published molecular docking scores depend on the receptor, ligand, software, search box, seed, and preparation choices; a paper reporting only the score has published a number with unknowable provenance. We ask whether such claims can be re-executed from their own published records. We introduce MERS-Dock, a 16-field Minimum Executable Reporting Set, and a deterministic E0-E4 executability ladder over audited field states. In 236 open-access SARS-CoV-2 main-protease docking papers, only 8.1% met the essential-field rule for direct re-execution (E3), 47.9% were blocked by a missing foundational field (E1), and none reached E4; mean field completeness was 49.1% and the search-box centre was reported by only 33.9%. We validated the audit against two independent human reviewers on a 65-paper stratified sample: inter-reviewer agreement was 92% (pooled Cohen kappa 0.87), and the automated agent matched humans on the execution-blocking fields while over-calling two non-blocking fields; the resulting E-class was 68% concordant with humans and, where it differed, human review lowered the executable count -- so the low-executability finding is confirmed, not inflated. Reporting did not improve over 2021-2026 (completeness vs year Spearman rho = -0.01). A bounded within-paper re-execution shows the reproduction gap is a box-coverage geometry effect, not box-size disclosure. We read E-class as an executability gate, not a reproducibility predictor, and release Mpro-DockExec as a traceable measurement layer for digital-library and evidence-synthesis systems deciding what is checkable in published computational claims.