Abstract
Molecular dynamics (MD) simulations have emerged as pivotal tools for deciphering the molecular mechanisms of Traditional Chinese Medicine (TCM), yet a comprehensive analysis of their global impact has not been conducted. We conducted a 20-year bibliometric analysis (2006-2025 December 31) of 6054 publications from the Web of Science Core Collection, Scopus and CNKI employing R packages and VOSviewer to map publication trends, collaborations, thematic evolution, and disease foci. Annual output surged from 1 article in 2006 to 1268 in 2024, representing a 1268-fold increase over the 19-year period (2006-2024). By December 31, 2025, the output for 2025 had already reached 1835 articles, indicating sustained momentum. China (46.8%), India (24.7%), and Saudi Arabia (9.9%) dominated research, with robust South-South collaborations (e.g., India-Saudi Arabia: weight = 229). Key journals included Journal of Biomolecular Structure & Dynamics (503 articles) and Phytomedicine (185 articles). Methodological shifts revealed progression from docking (2022) toward AI-driven bioinformatics (2024). Disease focus pivoted from chronic conditions (pre-2020) to infectious diseases (36.63% during COVID-19), then rebounded to cancer (+ 193% for breast cancer) and neurodegeneration (+ 182%).This computational renaissance positions MD simulations-augmented by AI and robust cross-regional collaboration-as indispensable for modernizing TCM. Future work must prioritize protocol standardization, open-data platforms that leverage global computational strengths, and translational validation to unlock TCM's full phytopharmacological potential.