发表机构
New Science Lab Nanjing Medical University（南京医科大学新科学实验室）
机构由 AI 辅助整理，请以论文原文为准。AI 中文总结
本研究通过审计50篇论文并重执行37项声明，量化了分子对接报告字段对可复现性的影响，发现受体结构是关键因素，并提出了经验字段权重用于NewScience证据评分。
AI 中文摘要
计算对接结果只有在分子系统和协议被明确指定时才能被重新执行，然而报告检查清单并未量化各个方法字段对报告得分的影响强度。我们将对50篇开放获取论文的跨度验证审计与受控单因素扰动、Vinardo评分函数检查以及覆盖7个蛋白家族中12个靶标的Vina交叉对接扩展相结合，并在本地和独立云基础设施上重新执行了37项已发表的声明。搜索相关字段的报告稀疏，但扰动盒子中心、盒子大小、穷尽性或随机种子产生的得分中位数绝对变化不超过0.08 kcal mol$^{-1}$；配体质子化和同一性分别产生0.19和0.29 kcal mol$^{-1}$的中位数变化，而受体结构产生的变化最大（1.02 kcal mol$^{-1}$；n = 85；P < 0.001），并且在确定性名称归一化后，116个唯一报告的配体字符串中有22%仍无法解析或存在歧义。这些测量为NewScience证据评分提供了经验字段权重，并确定了精确的受体结构、机器可解析的配体同一性和质子化状态作为主要报告要素；37次本地重执行中有29次和37次云重执行中有27次在报告得分的2.0 kcal mol$^{-1}$范围内，但这些描述性比率并不估计实验重复性或校准的复现概率。
英文摘要
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.
Comments29 pages, 8 figures, 6 tables. Retained derived data, verification code and source limitations included as ancillary files
