3.15 初稿

3.11 去北京的飞机上，跟老师们确认了下，还是先不费功夫去跟deepseek结合了，先把文章框架写出来
3.12-3.14 把文章框架大概写完了，有一些地方需要补实验：

MD部分

文献调研：类似文章中MD意义

  1. Exploring TβRI inhibitors from Arenaria kansuensis based on 3D-QSAR, molecular docking and molecular dynamics simulation methods and its anti-pulmonary fibrosis molecular mechanism validation - ScienceDirect
接在Docking（分析相互作用）之后，用rmsd,rmsf说明结合稳定“indicating that the binding mode between small molecules and proteins reached a stable state after 40ns” ； mmgbsa说明“which is high. It shows that the small molecule compound and protein bind well after the stable state is reached ”（不专业）
  1. Network pharmacology combines machine learning, molecular simulation dynamics and experimental validation to explore the mechanism of acetylbinankadsurin A in the treatment of liver fibrosis - ScienceDirect
通过RMSD分析结合的稳定性“We performed molecular dynamics simulations of the protein-ligand complexes after molecular docking to examine the stability” 
分析口袋部分残基的RMSF进一步确定结合的稳定性
  1. Sappanone A: A natural PDE4 inhibitor with dual anti-inflammatory and antioxidant activities from the heartwood of Caesalpinia sappan L. - ScienceDirect
接在虚筛之后，作为预测手段，进一步说明药靶结合（XX是XX的抑制剂）“In conclusion, sappanone A was further identified as a potential PDE4 inhibitor by the analysis of MD simulation of the sappanone A/4X0F complex.”
  1. Evaluation of in vitro and in silico anti-inflammatory potential of some selected medicinal plants of Bangladesh against cyclooxygenase-II enzyme - ScienceDirect
很详细，RMSD, RMSF, protein-ligand contact and hydrogen bond interaction 都作为独立部分进行讨论
HSBD-Manuscript draft-zyzhou-2025-3-17-raw.docx