AI 中文总结
研究探讨已发表分子对接声明的可重新执行性，引入MERS-Dock及可执行性阶梯，通过对236篇相关论文审核发现可执行性低，验证审核并分析结果，表明再现差距是几何效应，将E类作可执行性门，发布测量层助数字系统核查计算声明。
AI 中文摘要
已发表的分子对接分数取决于受体、配体、软件、搜索框、种子和制备选择；仅报告分数的论文发表的数字来源不可知。我们探讨此类声明能否根据其已发表记录重新执行。我们引入了MERS-Dock，一个包含16个字段的最小可执行报告集，以及一个针对审核字段状态的确定性E0-E4可执行性阶梯。在236篇开放获取的SARS-CoV-2主蛋白酶对接论文中，只有8.1%符合直接重新执行的基本字段规则（E3），47.9%因缺少基础字段而受阻（E1），没有一篇达到E4；平均字段完整性为49.1%，仅33.9%报告了搜索框中心。我们在一个65篇论文的分层样本上针对两名独立的人类评审员验证了审核：评审员间一致性为92%（合并科恩卡帕系数为0.87），自动化代理在执行受阻字段上与人类匹配，但多标记了两个非受阻字段；最终的E类与人类的一致性为68%，不同时，人工评审降低了可执行计数——因此低可执行性的发现得到证实，而非夸大。2021 - 2026年期间报告情况没有改善（完整性与年份的斯皮尔曼相关系数为 - 0.01）。有限的论文内重新执行表明，再现差距是盒覆盖几何效应，而非盒大小披露问题。我们将E类视为可执行性门，而非再现性预测指标，并发布Mpro-DockExec作为数字图书馆和证据综合系统的可追溯测量层，以决定已发表计算声明中哪些是可核查的。
英文摘要
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.
Comments19 pages, 6 figures. Data, code, and the MERS-Dock reporting standard: https://github.com/giapha/mpro-dockexec
