[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"detail-sidebar-cat-0-en-105":3,"doc-seo-291246-105":59,"doc-detail-291246-en":130},{"code":4,"msg":5,"data":6},0,"success",[7,13,18,23,28,33,38,43,48,51,55],{"id":8,"doc_module":4,"doc_module_name":9,"category_name":10,"show_sort_weight":11,"slug":12},1,"Document","Story & Novel",90,"story-novel",{"id":14,"doc_module":4,"doc_module_name":9,"category_name":15,"show_sort_weight":16,"slug":17},2,"Literature",80,"literature",{"id":19,"doc_module":4,"doc_module_name":9,"category_name":20,"show_sort_weight":21,"slug":22},4,"Exam",70,"exam",{"id":24,"doc_module":4,"doc_module_name":9,"category_name":25,"show_sort_weight":26,"slug":27},5,"Comic",60,"comic",{"id":29,"doc_module":4,"doc_module_name":9,"category_name":30,"show_sort_weight":31,"slug":32},6,"Technology",50,"technology",{"id":34,"doc_module":4,"doc_module_name":9,"category_name":35,"show_sort_weight":36,"slug":37},7,"Healthcare",40,"healthcare",{"id":39,"doc_module":4,"doc_module_name":9,"category_name":40,"show_sort_weight":41,"slug":42},8,"Research & Report",30,"research-report",{"id":44,"doc_module":4,"doc_module_name":9,"category_name":45,"show_sort_weight":46,"slug":47},9,"Religion & Spirituality",20,"religion-spirituality",{"id":46,"doc_module":4,"doc_module_name":9,"category_name":49,"show_sort_weight":46,"slug":50},"World Cup","world-cup",{"id":52,"doc_module":4,"doc_module_name":9,"category_name":53,"show_sort_weight":52,"slug":54},10,"Lifestyle","lifestyle",{"id":56,"doc_module":4,"doc_module_name":9,"category_name":57,"show_sort_weight":24,"slug":58},19,"General","general",{"code":4,"msg":60,"data":61},"ok",{"site_id":62,"language":63,"slug":64,"title":65,"keywords":66,"description":67,"schema_data":68,"social_meta":123,"head_meta":125,"extra_data":127,"updated_unix":129},105,"en","exploring-protein-conformations-and-functions-through-molecular-dynamics-simulations-and-machine-learning","Exploring Protein Conformations and Functions Through Molecular Dynamics Simulations and Machine Learning","","The dissertation investigates how protein conformation determines biological activity and how atomistic computational methods can reveal these relationships. It presents a machine learning framework for allostery in the diatom Phaeodactylum tricornutum aureochrome 1a and introduces PASSer for accurate allosteric site prediction. It further develops deep-learning approaches using variational autoencoders to learn low-dimensional representations of high-dimensional conformations, demonstrated on adenosine kinase and Vivid, plus adaptive sampling to accelerate conformational exploration.",{"@graph":69,"@context":122},[70,84,105],{"@type":71,"itemListElement":72},"BreadcrumbList",[73,77,79,82],{"item":74,"name":75,"@type":76,"position":8},"https://docshare.wps.com","Home","ListItem",{"item":78,"name":9,"@type":76,"position":14},"https://docshare.wps.com/document/",{"item":80,"name":40,"@type":76,"position":81},"https://docshare.wps.com/document/research-report/",3,{"item":83,"name":65,"@type":76,"position":19},"https://docshare.wps.com/document/exploring-protein-conformations-and-functions-through-molecular-dynamics-simulations-and-machine-learning/291246/",{"url":83,"name":65,"@type":85,"image":86,"author":91,"headline":65,"publisher":94,"fileFormat":97,"inLanguage":63,"description":67,"dateModified":98,"datePublished":99,"encodingFormat":97,"isAccessibleForFree":100,"interactionStatistic":101},"DigitalDocument",{"url":87,"@type":88,"width":89,"height":90},"https://docshare.wps.com/thumbnails/exploring-protein-conformations-and-functions-through-molecular-dynamics-simulations-and-machine-learning/291246.png","ImageObject",300,407,{"name":92,"@type":93},"Aurelia","Person",{"url":74,"name":95,"@type":96},"DocShare","Organization","application/pdf","2026-10-17","2026-09-17",true,{"@type":102,"interactionType":103,"userInteractionCount":52},"InteractionCounter",{"@type":104},"ViewAction",{"@type":106,"mainEntity":107},"FAQPage",[108,114,118],{"name":109,"@type":110,"acceptedAnswer":111},"What problem does the dissertation address regarding proteins?","Question",{"text":112,"@type":113},"It examines how protein tertiary structure and conformation influence biological activity, and how to study conformation and function computationally at the atomistic level.","Answer",{"name":115,"@type":110,"acceptedAnswer":116},"How is protein allostery studied in the first part of the dissertation?",{"text":117,"@type":113},"A machine learning-based framework is used to understand the allosteric process in the light-oxygen-voltage domain of Phaeodactylum tricornutum aureochrome 1a.",{"name":119,"@type":110,"acceptedAnswer":120},"What methods are used in the second part to explore protein conformations?",{"text":121,"@type":113},"Deep learning with variational autoencoders learns low-dimensional representations of high-dimensional conformations, along with an adaptive sampling method to accelerate exploration of conformational space.","https://schema.org",{"og:url":83,"og:type":124,"og:title":65,"og:site_name":95,"og:description":67},"article",{"robots":126,"canonical":83},"index,follow",{"doc_id":128,"site_id":62},291246,1789643865,{"code":4,"msg":5,"data":131},{"doc_id":128,"user_id":132,"nickname":92,"user_avatar":133,"doc_module":4,"category_id":39,"category_name":40,"doc_title":65,"doc_description":67,"doc_content":134,"file_id":135,"file_url":136,"file_type":137,"file_size":138,"view_count":52,"is_deleted":4,"is_public":8,"is_downloadable":8,"audit_status":8,"page_count":139,"language":140,"language_code":63,"site_id":62,"html_lang":63,"table_of_contents":141,"faqs":142,"seo_title":143,"seo_description":67,"update_tm":129,"read_time":144,"preview_page_count":4},1099514068365,"https://ap-avatar.wpscdn.com/avatar/10000253d8d9f28188e?x-image-process=image/resize,m_fixed,w_180,h_180&k=1794309523707217728","Southern Methodist University  \nSMU Scholar  \n\n| Chemistry Theses and Dissertations | Chemistry |\n| --- | --- |\n| Spring 2023\u003Cbr>Exploring Protein Conformations and Functions Through Molecular Dynamics Simulations and Machine Learning\u003Cbr>Hao Tian\u003Cbr>Southern Methodist University, [hhaootian@gmail.com](hhaootian@gmail.com)\u003Cbr>Follow this and additional works at: [https://scholar.smu.edu/hum_sci_chemistry_etds](https://scholar.smu.edu/hum_sci_chemistry_etds)\u003Cbr> Part of the Computational Chemistry Commons |  |\n\nRecommended Citation  \nTian, Hao, \"Exploring Protein Conformations and Functions Through Molecular Dynamics Simulations and Machine Learning\" (2023) . Chemistry Theses and Dissertations. 34.  \n[https://scholar.smu.edu/hum_sci_chemistry_etds/34](https://scholar.smu.edu/hum_sci_chemistry_etds/34)  \nThis Dissertation is brought to you for free and open access by the Chemistry at SMU Scholar. It has been accepted for inclusion in Chemistry Theses and Dissertations by an authorized administrator of SMU Scholar. For more information, please visit [http://digitalrepository.smu.edu](http://digitalrepository.smu.edu).  \nEXPLORING PROTEIN CONFORMATIONS AND FUNCTIONS  \nTHROUGH MOLECULAR DYNAMICS SIMULATIONS  \nAND MACHINE LEARNING  \nApproved by:  \n\n| Prof. Peng Tao\u003Cbr>Associate Professor |\n| --- |\n| Prof. Brian Zoltowski\u003Cbr>Associate Professor |\n| Prof. Devin Matthews\u003Cbr>Assistant Professor |\n\nProf. Eric Larson Associate Professor  \nEXPLORING PROTEIN CONFORMATIONS AND FUNCTIONS THROUGH MOLECULAR DYNAMICS SIMULATIONSAND MACHINE LEARNING  \nA Dissertation Presented to the Graduate Faculty of the  \nDedman College  \nSouthern Methodist University  \nin  \nPartial Fulfillment of the Requirements  \nfor the degree of  \nDoctor of Philosophy  \nwith a  \nMajor in Theoretical and Computational Chemistry  \nby  \nHao Tian  \nB.Eng., Chemical Engineering, Beijing University of Chemical Technology, China  \nMay 13, 2023  \nCopyright (2023)  \nHao Tian  \nAll Rights Reserved  \nAcknowledgments  \n“It was the best of times, it was the worst of times.” -Charles Dickens  \nIt was a unique journey to pursue a Ph.D. during the COVID-19 pandemic. I still remember the day I was required to go home and take online courses. It was a tough time in life and research, but I’m glad I made it eventually.  \nI would like to express my deepest gratitude to my advisor, Prof. Peng Tao, for his guidance and expertise in my Ph.D. studies. I would also like to thank my committee members, Prof. Devin Matthews, Prof. Eric Larson, and Prof. Brian Zoltowski, for their insightful critiques and valuable contributions to my research. I would like to extend my thanks to my fellow graduate students for their camaraderie and support. I am grateful tomy family for their unwavering love.  \nI want to thank my partner Xi Jiang for her love, tolerance, and patience. I would not go this far without her support.  \nThank you all for your commitment, dedication, and contributions to my academic and personal growth [throughout my Ph.D. study](throughout my Ph.D. study).  \nTian, Hao B.Eng. , Chemical Engineering, Beijing University of Chemical Technology, China  \nExploring Protein Conformations and Functions  Through Molecular Dynamics Simulations and Machine Learning  \nAdvisor: Prof. Peng Tao  \nDoctor of Philosophy degree conferred May 13, 2023 Dissertation completed April 21, 2023  \nProteins are essential biomacromolecules that perform a variety of critical functions in living organisms. The tertiary structure of a protein plays a crucial role in its biological activity as it determines how the protein interacts with other molecules. Consequently, understanding protein conformation and function is an important area of research with implications in medicine, biotechnology, and other fields.  \nThe first part of this dissertation focuses on protein allostery, a process by which proteins transmit perturbations caused by binding at one site to a distal site, thereby regulating activity. With the development ","cbCaie9Evrn6Veym","https://ap.wps.com/l/cbCaie9Evrn6Veym","pdf",76829818,183,"English","# CHAPTER 1 INTRODUCTION\n# CHAPTER 2 METHODOLOGIES\n## 2.1. Molecular Dynamics Simulations\n## 2.2. Trajectory Analysis\n## 2.3. Machine Learning\n## 2.4. Performance Assessment Criteria\n## 2.5. Markov State Model\n## 2.6. Machine","[{\"question\":\"What problem does the dissertation address regarding proteins?\",\"answer\":\"It examines how protein tertiary structure and conformation influence biological activity, and how to study conformation and function computationally at the atomistic level.\"},{\"question\":\"How is protein allostery studied in the first part of the dissertation?\",\"answer\":\"A machine learning-based framework is used to understand the allosteric process in the light-oxygen-voltage domain of Phaeodactylum tricornutum aureochrome 1a.\"},{\"question\":\"What methods are used in the second part to explore protein conformations?\",\"answer\":\"Deep learning with variational autoencoders learns low-dimensional representations of high-dimensional conformations, along with an adaptive sampling method to accelerate exploration of conformational space.\"}]","Exploring Protein Conformations and Functions Through Molecular Dynamics Simulations and Machine Learning | PDF",461]