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<span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Calibri; font-size: 16px;" class="">This is an announcement of </span><span class="outlook-search-highlight" style="font-family: Calibri; font-size: 16px; color: rgb(7, 7, 6);"><span class="outlook-search-highlight">Jacob</span></span><span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Calibri; font-size: 16px;" class=""> </span><span class="outlook-search-highlight" style="font-family: Calibri; font-size: 16px; color: rgb(7, 7, 6);"><span class="outlook-search-highlight">Williams</span></span><span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Calibri; font-size: 16px;" class="">'s </span><span class="outlook-search-highlight" style="font-family: Calibri; font-size: 16px; color: rgb(7, 7, 6);"><span class="outlook-search-highlight">Candidacy</span></span><span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Calibri; font-size: 16px;" class=""> Exam.</span><br class="" style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Calibri; font-size: 16px;">
<span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Calibri; font-size: 16px;" class="">===============================================</span><br class="" style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Calibri; font-size: 16px;">
<span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Calibri; font-size: 16px;" class="">Candidate: </span><span class="outlook-search-highlight" style="font-family: Calibri; font-size: 16px; color: rgb(7, 7, 6);"><span class="outlook-search-highlight">Jacob</span></span><span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Calibri; font-size: 16px;" class=""> </span><span class="outlook-search-highlight" style="font-family: Calibri; font-size: 16px; color: rgb(7, 7, 6);"><span class="outlook-search-highlight">Williams</span></span><br class="" style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Calibri; font-size: 16px;">
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<span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Calibri; font-size: 16px;" class="">Date: Monday, May 06, 2024</span><br class="" style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Calibri; font-size: 16px;">
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<span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Calibri; font-size: 16px;" class="">Time: 10 am CT</span><br class="" style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Calibri; font-size: 16px;">
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<span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Calibri; font-size: 16px;" class="">Remote Location: </span><a href="https://urldefense.com/v3/__https://uchicago.zoom.us/j/93007490832?pwd=K1BZRHdKS0RqQ09qc1l2T2JQUHMxdz09__;!!BpyFHLRN4TMTrA!7FTiA9YmUUDmMewPDb7-I66I8I-mwk419RZQZ_n5Vh0fu1Y40c7JCyUNaKIa7M0GHWQaQh_UI6BuEy79_q9bRi4ScFVd7JsqLqOt$" class="" title="https://urldefense.com/v3/__https://uchicago.zoom.us/j/93007490832?pwd=K1BZRHdKS0RqQ09qc1l2T2JQUHMxdz09__;!!BpyFHLRN4TMTrA!7FTiA9YmUUDmMewPDb7-I66I8I-mwk419RZQZ_n5Vh0fu1Y40c7JCyUNaKIa7M0GHWQaQh_UI6BuEy79_q9bRi4ScFVd7JsqLqOt$" style="font-family: Calibri; font-size: 16px;">https://uchicago.zoom.us/j/93007490832?pwd=K1BZRHdKS0RqQ09qc1l2T2JQUHMxdz09</a><span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Calibri; font-size: 16px;" class=""> Meeting
ID: 930 0749 0832 Passcode: 815521</span><br class="" style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Calibri; font-size: 16px;">
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<span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Calibri; font-size: 16px;" class="">Location: JCL 390</span><br class="" style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Calibri; font-size: 16px;">
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<span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Calibri; font-size: 16px;" class="">Title: Machine Learning and NMR Spectroscopy</span><br class="" style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Calibri; font-size: 16px;">
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<span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Calibri; font-size: 16px;" class="">Abstract: The recent introduction of AlphaFold (AF) has fundamentally changed our ability to predict the structure of proteins from their primary
sequence of amino acids. The AlphaFold Protein Structure Database currently contains over 200 million predicted structures. As AI protein prediction continues to advance, we examine the potential of hybrid techniques that combine experiment and computation
that may yield more accurate structures than AI alone with significantly reduced experimental burden. We present a heuristic comparing N-edited NOESY spectra and AlphaFold predicted structures that seeks to determine whether the predicted structure reasonably
describes the true structure of the protein. Using verified structures from the Protein Data Bank (PDB) and the corresponding NMR data from the Biological Magnetic Resonance Data Bank (BMRB), we seek to find a simple way to compare AlphaFold predictions to
measured NMR data which informs our understanding of the quality of AlphaFold predictions. Our heuristics are similar in nature to distance restraints, in that they use the peaks from the NOESY spectra to determine which residues in a protein are likely to
be nearby in physical space. They are fed into a small machine learning model which learns by comparing the PDB and AlphaFold structures for the same protein, to construct a system which can validate predicted structures relative to the data. We will also
consider ways to refine AlphaFold predictions, updating the structures themselves to create more likely configurations given the observed NMR spectra. This refinement will likely take the form of deep learning models such as energy-based models. The future
of structure elucidation for proteins and other large molecules likely lies with hybrid methods that combine fast and accurate AI and ML models with a small set of experiments that will validate and refine structures.</span><br class="" style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Calibri; font-size: 16px;">
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<span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Calibri; font-size: 16px;" class="">Advisors: Rebecca Willett</span><br class="" style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Calibri; font-size: 16px;">
<br class="" style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Calibri; font-size: 16px;">
<span style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Calibri; font-size: 16px;" class="">Committee Members: Ian Foster, Risi Kondor, and Rebecca Willett</span><br class="" style="caret-color: rgb(33, 33, 33); color: rgb(33, 33, 33); font-family: Calibri; font-size: 16px;">
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