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However, protein function is not solely determined by static three-dimensional structures but is fundamentally governed by dynamic transitions between multiple conformational states. This shift from static to multi-state representations is crucial for understanding the mechanistic basis of protein function and regulation. This review outlines the fundamental concepts of protein dynamic conformations, surveys recent computational advances in modeling these dynamics in the post-AlphaFold era, and highlights key challenges, including data limitations, methodological constraints, and evaluation metrics. We also discuss potential strategies to address these challenges and explore future research directions to deepen our understanding of protein dynamics and their functional implications. This work aims to provide insights and perspectives to facilitate the ongoing development of protein conformation studies in the era of artificial intelligence-driven structural biology.<\/jats:p>","DOI":"10.1093\/bib\/bbaf340","type":"journal-article","created":{"date-parts":[[2025,7,15]],"date-time":"2025-07-15T17:15:24Z","timestamp":1752599724000},"source":"Crossref","is-referenced-by-count":31,"title":["Beyond static structures: protein dynamic conformations modeling in the post-AlphaFold era"],"prefix":"10.1093","volume":"26","author":[{"given":"Xinyue","family":"Cui","sequence":"first","affiliation":[{"name":"College of Information Engineering, Zhejiang University of Technology , 288 Liuhe Road, Hangzhou 310023, Zhejiang ,","place":["China"]}]},{"given":"Lingyu","family":"Ge","sequence":"additional","affiliation":[{"name":"College of Information Engineering, Zhejiang University of Technology , 288 Liuhe Road, Hangzhou 310023, Zhejiang ,","place":["China"]}]},{"given":"Xia","family":"Chen","sequence":"additional","affiliation":[{"name":"College of Information Engineering, Zhejiang University of Technology , 288 Liuhe Road, Hangzhou 310023, Zhejiang ,","place":["China"]}]},{"given":"Zexin","family":"Lv","sequence":"additional","affiliation":[{"name":"College of Information Engineering, Zhejiang University of Technology , 288 Liuhe Road, Hangzhou 310023, Zhejiang ,","place":["China"]}]},{"given":"Suhui","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Information Engineering, Zhejiang University of Technology , 288 Liuhe Road, Hangzhou 310023, Zhejiang ,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6839-1923","authenticated-orcid":false,"given":"Xiaogen","family":"Zhou","sequence":"additional","affiliation":[{"name":"College of Information Engineering, Zhejiang University of Technology , 288 Liuhe Road, Hangzhou 310023, Zhejiang 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