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Among them, in-depth exploration of ligand-driven protein dynamics contributes to an optimal understanding of protein function, which is particularly relevant to drug discovery. Hence, a wide range of computational tools have been designed to investigate the important dynamic information in proteins. However, performing and analyzing protein dynamics is still challenging due to the complicated operation steps, giving rise to great difficulty, especially for nonexperts. Moreover, there is a lack of web protocol to provide online facility to investigate and visualize ligand-driven protein dynamics. To this end, in this study, we integrated several bioinformatic tools to develop a protocol, named Ligand and Receptor Molecular Dynamics (LARMD, http:\/\/chemyang.ccnu.edu.cn\/ccb\/server\/LARMD\/ and http:\/\/agroda.gzu.edu.cn:9999\/ccb\/server\/LARMD\/), for profiling ligand-driven protein dynamics. To be specific, estrogen receptor (ER) was used as a case to reveal ER\u03b2-selective mechanism, which plays a vital role in the treatment of inflammatory diseases and many types of cancers in clinical practice. Two different residues (Ile373\/Met421 and Met336\/Leu384) in the pocket of ER\u03b2\/ER\u03b1 were the significant determinants for selectivity, especially Met336 of ER\u03b2. The helix H8, helix H11 and H7-H8 loop influenced the migration of selective agonist (WAY-244). These computational results were consistent with the experimental results. Therefore, LARMD provides a user-friendly online protocol to study the dynamic property of protein and to design new ligand or site-directed mutagenesis.<\/jats:p>","DOI":"10.1093\/bib\/bbz141","type":"journal-article","created":{"date-parts":[[2019,10,16]],"date-time":"2019-10-16T22:12:30Z","timestamp":1571263950000},"page":"2206-2218","source":"Crossref","is-referenced-by-count":102,"title":["LARMD: integration of bioinformatic resources to profile ligand-driven protein dynamics with a case on the activation of estrogen receptor"],"prefix":"10.1093","volume":"21","author":[{"given":"Jing-Fang","family":"Yang","sequence":"first","affiliation":[{"name":"Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P.R.China"},{"name":"International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University\uff0cWuhan, 430079, China"}]},{"given":"Fan","family":"Wang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P.R.China"},{"name":"International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University\uff0cWuhan, 430079, China"}]},{"given":"Yu-Zong","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117543"}]},{"given":"Ge-Fei","family":"Hao","sequence":"additional","affiliation":[{"name":"Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P.R.China"},{"name":"International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University\uff0cWuhan, 430079, China"},{"name":"State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang 550025, P. 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