Computational renaissance in herbal medicine: A 20-year bibliometric deciphering of molecular dynamics simulations reshaping traditional Chinese medicine drug discovery

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.