James Fraser, PhD · School of Pharmacy

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Additionally, I aim to improve the evaluation of research in hiring and promotion and ensure that our research agenda aligns well with staff and learner career goals. My" /> <link rel="canonical" href="https://pharmacy.ucsf.edu/james-fraser" /> <meta property="og:site_name" content="UCSF School of Pharmacy" /> <meta property="og:type" content="website" /> <meta property="og:title" content="James Fraser, PhD · Department Chair and Professor" /> <meta property="og:url" content="https://pharmacy.ucsf.edu/james-fraser" /> <meta property="og:description" content="Department of Bioengineering and Therapeutic Sciences · I coordinate the School’s broad research efforts, aiming to catalyze collaborations across labs, departments, the university, and outside institutions. Additionally, I aim to improve the evaluation of research in hiring and promotion and ensure that our research agenda aligns well with staff and learner career goals. My research is focused on discovering the macromolecular structure and dynamics of proteins—defining conformational states essential for function and understanding transitions between these states. I also chair the Department of Bioengineering and Therapeutic Sciences. 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Prien Professor</div> </div> <div class="views-field views-field-field-person-office-dean-title"> <div class="field-content"></div> </div> </div> </div> </div> </div> </div> <div class="panel-separator"></div><div class="panel-pane pane-views-panes pane-ucsf-person-profile-panel-pane-5" > <div class="pane-content"> <div class="view view-ucsf-person-profile view-id-ucsf_person_profile view-display-id-panel_pane_5 view-dom-id-3208f83da9a515d0e4745f9c4492de47"> <div class="view-content"> <div class="views-row views-row-1 views-row-odd views-row-first views-row-last"> <div class="views-field views-field-field-person-primary-dept"> <div class="field-content"><a href="https://bts.ucsf.edu/">Department of Bioengineering and Therapeutic Sciences</a></div> </div> </div> </div> </div> </div> </div> </div> </div> <div class="moscone-container moscone-column-content clearfix"> <div class="moscone-column-content-region moscone-sidebar panel-panel"> <div class="moscone-column-content-region-inner 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srcset="/sites/pharmacy.ucsf.edu/files/styles/pharmacy_square_half/public/person/photo/james_fraser_2023_hirez.jpg?itok=CxPJkxTt&timestamp=1729615173 1x, /sites/pharmacy.ucsf.edu/files/styles/pharmacy_square_0_75x/public/person/photo/james_fraser_2023_hirez.jpg?itok=lUeFjtx8&timestamp=1729615173 2x, /sites/pharmacy.ucsf.edu/files/styles/pharmacy_square_1_5x/public/person/photo/james_fraser_2023_hirez.jpg?itok=WTuknrZ5&timestamp=1729615173 3x" media="(min-width: 656px) and (max-width: 1024px)" /> <source srcset="/sites/pharmacy.ucsf.edu/files/styles/pharmacy_square_quarter/public/person/photo/james_fraser_2023_hirez.jpg?itok=XlcNSJHs&timestamp=1729615173 1x, /sites/pharmacy.ucsf.edu/files/styles/pharmacy_square_half/public/person/photo/james_fraser_2023_hirez.jpg?itok=CxPJkxTt&timestamp=1729615173 2x, /sites/pharmacy.ucsf.edu/files/styles/pharmacy_square_0_75x/public/person/photo/james_fraser_2023_hirez.jpg?itok=lUeFjtx8&timestamp=1729615173 3x" media="(min-width: 481px) and (max-width: 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(max-width: 430px)" />  <img src="/sites/pharmacy.ucsf.edu/files/styles/pharmacy_square_third/public/person/photo/james_fraser_2023_hirez.jpg?itok=gueYywzm&timestamp=1729615173" alt="Fraser" title="" /> </picture> <div class="field field-name-field-image-credit-term field-type-taxonomy-term-reference field-label-hidden"> <div class="field-items"> <div class="field-item even">Nico Oved</div> </div> </div> </div> </div> </div></div></div> </div> </div> <div class="panel-separator"></div><div class="panel-pane pane-entity-field pane-node-field-person-email" > <div class="pane-content"> <div class="field field-name-field-person-email field-type-email field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/cdn-cgi/l/email-protection#f89299959d8bd69e8a998b9d8ab88d9b8b9ed69d9c8d"><span class="__cf_email__" data-cfemail="6f050e020a1c41091d0e1c0a1d2f1a0c1c09410a0b1a">[email protected]</span></a></div></div></div> </div> </div> <div class="panel-separator"></div><div class="panel-pane pane-views-panes pane-ucsf-person-profile-panel-pane-7" > <div class="pane-content"> <div class="view view-ucsf-person-profile view-id-ucsf_person_profile view-display-id-panel_pane_7 view-dom-id-4a7e386428f6347cf2ef1da3b5434930"> <div class="view-content"> <div class="views-row views-row-1 views-row-odd views-row-first views-row-last"> <div class="views-field views-field-field-campus-phone"> <div class="field-content">Phone: +1 415 493-8421</div> </div> <div class="views-field views-field-field-person-fax"> <div class="field-content">Fax: +1 415 514-9736</div> </div> </div> </div> </div> </div> </div> <div class="panel-separator"></div><div class="panel-pane pane-token pane-node-field-person-address-postal" > <div class="pane-content"> <div class="street-block"><div class="thoroughfare">600 16th Street, Rm 001</div> <div class="premise">UCSF Box 2240</div></div> <div class="addressfield-container-inline locality-block country-US"><span class="locality">San Francisco</span>, <span class="state">CA</span> <span class="postal-code">94158</span></div> <span class="country">United States</span> </div> </div> <div class="panel-separator"></div><div class="panel-pane pane-views-panes pane-ucsf-person-profile-panel-pane-12" > <h2 class="pane-title">Links</h2> <div class="pane-content"> <div class="view view-ucsf-person-profile view-id-ucsf_person_profile view-display-id-panel_pane_12 view-dom-id-379712d05d295e47f832fef88ec1af1b"> <div class="view-content"> <div class="views-row views-row-1 views-row-odd views-row-first views-row-last"> <span class="views-field views-field-field-person-links"> <span class="field-content"><a href="https://fraserlab.com/" target="_blank">Fraser Lab</a></span> </span> <span class="views-field views-field-field-profiles-link"> <span class="field-content"><a href="https://profiles.ucsf.edu/james.fraser">UCSF Profiles</a></span> </span> </div> </div> </div> </div> </div> <div class="panel-separator"></div><div class="panel-pane pane-views-panes pane-ucsf-person-profile-panel-pane-24" > <div class="pane-content"> <div class="view view-ucsf-person-profile view-id-ucsf_person_profile view-display-id-panel_pane_24 view-dom-id-0c44d6b05edcd5d4b59ebd11a7fe3dda"> <div class="view-content"> <div> <h2>Affiliations</h2> </div> </div> <div class="view-footer"> <div class="view view-ucsf-person-profile view-id-ucsf_person_profile view-display-id-panel_pane_16 view-dom-id-b5dadaece79db73c2a5be9c73f6d8653"> </div><div class="view view-ucsf-person-profile view-id-ucsf_person_profile view-display-id-panel_pane_18 view-dom-id-c808483cebf94b0d642ce3ba7481c5ad"> <div class="view-header"> <h3>Education programs</h3> </div> <div class="view-content"> <div class="views-row views-row-1"> <a href="http://ccb.ucsf.edu/">Chemistry and Chemical Biology Graduate Program (CCB)</a> </div> <div class="views-row views-row-2"> <a href="https://biophysics.ucsf.edu/">Biophysics Graduate Program (BP)</a> </div> <div class="views-row views-row-3"> <a href="https://pspg.ucsf.edu">Pharmaceutical Sciences and Pharmacogenomics Graduate Program (PSPG)</a> </div> </div> </div><div class="view view-ucsf-person-profile view-id-ucsf_person_profile view-display-id-panel_pane_19 view-dom-id-e5e4d343ac99586055693ac7ce7f05f9"> <div class="view-header"> <h3>UCSF centers, institutes, and research programs</h3> </div> <div class="view-content"> <div class="views-row views-row-1"> <a href="https://qbi.ucsf.edu/">Quantitative Biosciences Institute (QBI)</a> </div> </div> </div><div class="view view-ucsf-person-profile view-id-ucsf_person_profile view-display-id-panel_pane_20 view-dom-id-75e2745c336876937672283c40c3ed1b"> </div><div class="view view-ucsf-person-profile view-id-ucsf_person_profile view-display-id-panel_pane_21 view-dom-id-0704b63d78fb194e42900837c87e1be4"> </div><div class="view view-ucsf-person-profile view-id-ucsf_person_profile view-display-id-panel_pane_22 view-dom-id-f8670c4625a9777be96acb98033b2131"> </div><div class="view view-ucsf-person-profile view-id-ucsf_person_profile view-display-id-panel_pane_23 view-dom-id-b9af7633937183ad1c51915c8a771107"> </div> </div> </div> </div> </div> </div> </div> <div class="moscone-column-content-region moscone-content panel-panel"> <div class="moscone-column-content-region-inner moscone-content-inner panel-panel-inner"> <div class="panel-pane pane-entity-field pane-node-field-person-what-i-do-text" > <h2 class="pane-title">What I do</h2> <div class="pane-content"> <div class="field field-name-field-person-what-i-do-text field-type-text-long field-label-hidden"><div class="field-items"><div class="field-item even"><p>I coordinate the School’s broad <a href="/research">research efforts</a>, aiming to catalyze collaborations across labs, departments, the university, and outside institutions. Additionally, I aim to improve the evaluation of research in hiring and promotion and ensure that our research agenda aligns well with staff and learner career goals.</p> <p>My research is focused on discovering the macromolecular structure and dynamics of proteins—defining conformational states essential for function and understanding transitions between these states.</p> <p>I also chair the <a href="https://bts.ucsf.edu">Department of Bioengineering and Therapeutic Sciences</a>. Details: <a href="https://bts.ucsf.edu/about/administration">Administration</a>.</p></div></div></div> </div> </div> <div class="panel-separator"></div><div class="panel-pane pane-views-panes pane-ucsf-person-profile-panel-pane-8 pane-float-left-fifty-departmental-research-area pane-float-left-fifty" > <h2 class="pane-title">Departmental research area</h2> <div class="pane-content"> <div class="view view-ucsf-person-profile view-id-ucsf_person_profile view-display-id-panel_pane_8 view-dom-id-65797660fb2097219b80d33480437ad5"> <div class="view-content"> <div class="views-row views-row-1 views-row-odd views-row-first views-row-last"> <div class="views-field views-field-field-research-area"> <div class="field-content"><a href="https://bts.ucsf.edu/research/computational-biology-systems-pharmacology">computational biology and systems pharmacology</a></div> </div> </div> </div> </div> </div> </div> <div class="panel-separator"></div><div class="panel-pane pane-token pane-node-field-person-dept-expertise-spec pane-float-left-fifty-my-research-expertise pane-float-left-fifty" > <h2 class="pane-title">My research expertise</h2> <div class="pane-content"> evolution, protein structure, protein conformational dynamics, x-ray crystallography, nuclear magnetic resonance (NMR), bioengineering </div> </div> <div class="panel-separator"></div><div class="panel-pane pane-views-panes pane-ucsf-person-profile-panel-pane-14" > <div class="pane-content"> <div class="view view-ucsf-person-profile view-id-ucsf_person_profile view-display-id-panel_pane_14 view-dom-id-6593beac65176485ae7cb347562191f1"> <div class="view-content"> <div> <h2>Professional background</h2> </div> </div> <div class="view-footer"> <div class="view view-ucsf-person-profile view-id-ucsf_person_profile view-display-id-panel_pane_2 view-dom-id-150f5c3fa5cdd315afd5832b5f85a9bf"> <div class="view-header"> <h3>Degrees</h3> </div> <div class="view-content"> <div class="views-row views-row-1"> PhD, Molecular and Cell Biology, University of California, Berkeley, <span class="date-display-single" property="dc:date" datatype="xsd:dateTime" content="2010-01-01T00:00:00-08:00">2010</span> </div> <div class="views-row views-row-2"> BSc, Biology, McGill University, <span class="date-display-single" property="dc:date" datatype="xsd:dateTime" content="2005-01-01T00:00:00-08:00">2005</span> </div> </div> </div><div class="view view-ucsf-person-profile view-id-ucsf_person_profile view-display-id-panel_pane_13 view-dom-id-99f4657be82c8b897899da9aa52c36a3"> </div><div class="view view-ucsf-person-profile view-id-ucsf_person_profile view-display-id-panel_pane_15 view-dom-id-7f8a349158ddab905658a81e9a6b6f4f"> </div><div class="view view-ucsf-person-profile view-id-ucsf_person_profile view-display-id-panel_pane_17 view-dom-id-ffee38dbb182e1ff72521991a9d32b07"> </div> </div> </div> </div> </div> <div class="panel-separator"></div><div class="panel-pane pane-entity-field pane-node-field-person-research-biography" > <h2 class="pane-title">Biography</h2> <div class="pane-content"> <div class="field field-name-field-person-research-biography field-type-text-long field-label-hidden"><div class="field-items"><div class="field-item even"><p>The long-term goals of our research are to understand how protein conformational ensembles are reshaped by perturbations, such as mutation and ligand binding, and to quantify how these perturbations impact protein function and organismal fitness. To accomplish these goals, we create new computational and biophysical approaches to study how proteins move between different conformational states. As a graduate student, with Tom Alber at UC Berkeley, James established room temperature X-ray data collection techniques and electron density sampling strategies to define protein conformational ensembles essential for catalysis. Prior to starting an independent position at UCSF, he was a visiting EMBO Short Term Fellow in the lab of Dan Tawfik at the Weizmann Institute of Science in Israel and developed expertise in directed evolution and high-throughput assays of enzymatic or binding activity. In 2011, James started his independent research career as a QB3 at UCSF Fellow and in 2013 was appointed as an Assistant Professor of Bioengineering and Therapeutic Sciences. At UCSF, his lab continue to pioneer new methods for extracting the maximal information from X-ray diffraction experiments and electron density maps. Additionally, the group uses two complementary approaches to study the relationship between protein conformational ensembles and function. To dissect consequences of mutations on organismal fitness, we use high-throughput systems biology and biophysical methods to analyze large sets of clinically or biophysically interesting mutations. To improve our ability to engineer new protein functions, we investigate changes to the conformational ensemble as new enzymatic and binding functions emerge from directed evolution studies.</p> </div></div></div> </div> </div> <div class="panel-separator"></div><div class="panel-pane pane-views-panes pane-ucsf-person-profile-panel-pane-9" > <h2 class="pane-title">Research keywords</h2> <div class="pane-content"> <div class="view view-ucsf-person-profile view-id-ucsf_person_profile view-display-id-panel_pane_9 columns-3 view-dom-id-f40daf06e9ac02cdb97bbe3e22b93107"> <div class="view-content"> <div class="views-row views-row-1 views-row-odd views-row-first views-row-last"> <div class="views-field views-field-field-person-keywords-profiles"> <div class="field-content"><div class="item-list"><ul><li class="first">evolution</li> <li>protein structure</li> <li>Protein Conformational Dynamics</li> <li>x-ray crystallography</li> <li>NMR</li> <li>bioengineering</li> <li>Protein Conformation</li> <li>Chitin</li> <li>Tetrahydrofolate Dehydrogenase</li> <li>proteins</li> <li>X-Ray Diffraction</li> <li>Directed Molecular Evolution</li> <li>Protein Databases</li> <li>Molecular Dynamics Simulation</li> <li>Molecular Models</li> <li>Crystallography, X-Ray</li> <li>Cryoelectron Microscopy</li> <li>Proto-Oncogene Proteins c-met</li> <li>Cyclophilin A</li> <li>Temperature</li> <li class="last">Chitinases</li> </ul></div></div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div class="moscone-container moscone-footer clearfix panel-panel"> <div class="moscone-container-inner moscone-footer-inner panel-panel-inner"> <div class="panel-pane pane-block pane-quicktabs-quicktabs-pub-news-media" > <div class="pane-content"> <div id="quicktabs-quicktabs_pub_news_media" class="quicktabs-wrapper quicktabs-style-nostyle"><div class="item-list"><ul class="quicktabs-tabs quicktabs-style-nostyle"><li class="active first"><a href="/james-fraser?qt-quicktabs_pub_news_media=0#qt-quicktabs_pub_news_media" id="quicktabs-tab-quicktabs_pub_news_media-0" class="quicktabs-tab quicktabs-tab-view quicktabs-tab-view-person-related-items-panel-pane-1 active">News</a></li> <li><a href="/james-fraser?qt-quicktabs_pub_news_media=1#qt-quicktabs_pub_news_media" id="quicktabs-tab-quicktabs_pub_news_media-1" class="quicktabs-tab quicktabs-tab-view quicktabs-tab-view-person-related-items-panel-pane-2 active">Media Coverage</a></li> <li class="last"><a href="/james-fraser?qt-quicktabs_pub_news_media=2#qt-quicktabs_pub_news_media" id="quicktabs-tab-quicktabs_pub_news_media-2" class="quicktabs-tab quicktabs-tab-view quicktabs-tab-view-ucsf-person-profile-panel-pane-4 active">Honors & Awards</a></li> </ul></div><div id="quicktabs-container-quicktabs_pub_news_media" class="quicktabs_main quicktabs-style-nostyle"><div id="quicktabs-tabpage-quicktabs_pub_news_media-0" class="quicktabs-tabpage "><div class="view view-person-related-items view-id-person_related_items view-display-id-panel_pane_1 view-dom-id-59342ca3b3ac2c285b325ef5f54d6d6d"> <div class="view-content"> <table class="views-table cols-0"> <tbody> <tr class="odd views-row-first"> <td class="views-field views-field-counter"> 1. </td> <td class="views-field views-field-title"> <a href="/news/2024/12/year-review-top-5-milestones-2024">Year in Review: Top 5 Milestones of 2024</a> </td> </tr> <tr class="even"> <td class="views-field views-field-counter"> 2. </td> <td class="views-field views-field-title"> <a href="/news/2024/10/ucsf-school-pharmacy-leads-30m-award-speed-drug-development-ai">UCSF School of Pharmacy Leads $30M Award to Speed Drug Development with AI</a> </td> </tr> <tr class="odd"> <td class="views-field views-field-counter"> 3. </td> <td class="views-field views-field-title"> <a href="/news/2023/09/update-dean-putting-plans-action">Update from the Dean: Putting plans in action</a> </td> </tr> <tr class="even"> <td class="views-field views-field-counter"> 4. </td> <td class="views-field views-field-title"> <a href="/news/2023/08/fraser-named-chair-ucsf-department-bioengineering-therapeutic-sciences">Fraser named chair of UCSF Department of Bioengineering and Therapeutic Sciences</a> </td> </tr> <tr class="odd"> <td class="views-field views-field-counter"> 5. </td> <td class="views-field views-field-title"> <a href="/news/2022/12/update-dean-ongoing-excellence-new-frontiers">Update from the Dean: Ongoing excellence and new frontiers</a> </td> </tr> <tr class="even"> <td class="views-field views-field-counter"> 6. </td> <td class="views-field views-field-title"> <a href="/news/2022/10/new-era-science-practice-ucsf">A new era for science and practice at UCSF</a> </td> </tr> <tr class="odd"> <td class="views-field views-field-counter"> 7. </td> <td class="views-field views-field-title"> <a href="/news/2022/08/behind-enemy-lines">Behind enemy lines</a> </td> </tr> <tr class="even"> <td class="views-field views-field-counter"> 8. </td> <td class="views-field views-field-title"> <a href="/news/2022/06/diaz-honored-edison-t-uno-award-public-service">Díaz honored with Edison T. Uno Award for Public Service</a> </td> </tr> <tr class="odd"> <td class="views-field views-field-counter"> 9. </td> <td class="views-field views-field-title"> <a href="/news/2020/11/update-dean-community-during-challenging-times">Update from the Dean: Community during challenging times</a> </td> </tr> <tr class="even"> <td class="views-field views-field-counter"> 10. </td> <td class="views-field views-field-title"> <a href="/news/2020/10/resistant-bacteria-meet-their-match-custom-antibiotics">Resistant bacteria meet their match with custom antibiotics</a> </td> </tr> <tr class="odd"> <td class="views-field views-field-counter"> 11. </td> <td class="views-field views-field-title"> <a href="/news/2020/10/labs-juggle-community-distance-during-covid-19">Labs juggle community, distance during COVID-19</a> </td> </tr> <tr class="even"> <td class="views-field views-field-counter"> 12. </td> <td class="views-field views-field-title"> <a href="/news/2020/08/update-dean-back-school">Update from the Dean: Back to school</a> </td> </tr> <tr class="odd"> <td class="views-field views-field-counter"> 13. </td> <td class="views-field views-field-title"> <a href="/news/2020/07/how-targeting-key-sars-cov-2-enzyme-could-lead-antiviral-drug">How targeting a key SARS-CoV-2 enzyme could lead to an antiviral drug</a> </td> </tr> <tr class="even"> <td class="views-field views-field-counter"> 14. </td> <td class="views-field views-field-title"> <a href="/news/2020/04/update-dean-looking-forward-recovery">Update from the Dean: Looking forward to recovery</a> </td> </tr> <tr class="odd"> <td class="views-field views-field-counter"> 15. </td> <td class="views-field views-field-title"> <a href="/news/2020/04/overcoming-disease-moving-pictures-molecular-building-blocks">Overcoming disease with moving pictures and molecular building blocks</a> </td> </tr> <tr class="even"> <td class="views-field views-field-counter"> 16. </td> <td class="views-field views-field-title"> <a href="/news/2019/05/update-dean-may-2019">Update from the Dean – May 2019</a> </td> </tr> <tr class="odd"> <td class="views-field views-field-counter"> 17. </td> <td class="views-field views-field-title"> <a href="/news/2019/01/fraser-appointed-bowes-biomedical-investigator-program">Fraser appointed to Bowes Biomedical Investigator Program</a> </td> </tr> <tr class="even"> <td class="views-field views-field-counter"> 18. </td> <td class="views-field views-field-title"> <a href="/news/2015/03/update-dean-springsummer-2015">Update from the Dean - Spring/Summer 2015</a> </td> </tr> <tr class="odd"> <td class="views-field views-field-counter"> 19. </td> <td class="views-field views-field-title"> <a href="/news/2014/05/update-dean-springsummer-2014">Update from the Dean - Spring/Summer 2014</a> </td> </tr> <tr class="even"> <td class="views-field views-field-counter"> 20. </td> <td class="views-field views-field-title"> <a href="/news/2014/04/fraser-named-searle-scholar-will-shine-new-light-protein-shapeshifting">Fraser named Searle Scholar, will shine new light on protein shapeshifting</a> </td> </tr> <tr class="odd views-row-last"> <td class="views-field views-field-counter"> 21. </td> <td class="views-field views-field-title"> <a href="/news/2013/11/update-dean-fall-2013">Update from the Dean - Fall 2013</a> </td> </tr> </tbody> </table> </div> </div></div><div id="quicktabs-tabpage-quicktabs_pub_news_media-1" class="quicktabs-tabpage quicktabs-hide"><div class="view view-person-related-items view-id-person_related_items view-display-id-panel_pane_2 view-dom-id-ed00044137c6c6800e8e2da0af53f041"> <div class="view-content"> <table class="views-table cols-0"> <tbody> <tr class="odd views-row-first"> <td class="views-field views-field-counter"> 1. </td> <td class="views-field views-field-title"> <a href="/media-coverage/ai-has-designed-bacteria-killing-proteins-scratch-they-work">AI has designed bacteria-killing proteins from scratch—and they work</a> </td> </tr> <tr class="even"> <td class="views-field views-field-counter"> 2. </td> <td class="views-field views-field-title"> <a href="/media-coverage/where-are-drugs-beat-covid-next-pandemic">Where are drugs to beat COVID—and the next pandemic?</a> </td> </tr> <tr class="odd"> <td class="views-field views-field-counter"> 3. </td> <td class="views-field views-field-title"> <a href="/media-coverage/genetic-shortcut-help-visualize-proteins-work">A genetic shortcut to help visualize proteins at work</a> </td> </tr> <tr class="even views-row-last"> <td class="views-field views-field-counter"> 4. </td> <td class="views-field views-field-title"> <a href="/media-coverage/customizable-synthetic-antibiotic-outmaneuvers-resistant-bacteria">Customizable synthetic antibiotic outmaneuvers resistant bacteria</a> </td> </tr> </tbody> </table> </div> </div></div><div id="quicktabs-tabpage-quicktabs_pub_news_media-2" class="quicktabs-tabpage quicktabs-hide"><div class="view view-ucsf-person-profile view-id-ucsf_person_profile view-display-id-panel_pane_4 view-dom-id-c89e831af027261febedbbfa114d63ad"> <div class="view-content"> <table class="views-table cols-0"> <tbody> <tr class="odd views-row-first"> <td class="views-field views-field-counter"> 1. </td> <td class="views-field views-field-field-profiles-honors-awards"> W.H. and W.L. Bragg Prize, International Union of Crystallography, 2020 </td> </tr> <tr class="even"> <td class="views-field views-field-counter"> 2. </td> <td class="views-field views-field-field-profiles-honors-awards"> Byers Award in Basic Science, UCSF, 2020 </td> </tr> <tr class="odd"> <td class="views-field views-field-counter"> 3. </td> <td class="views-field views-field-field-profiles-honors-awards"> Packard Fellow, The David and Lucille Packard Foundation, 2014-2019 </td> </tr> <tr class="even"> <td class="views-field views-field-counter"> 4. </td> <td class="views-field views-field-field-profiles-honors-awards"> Searle Scholar, Kinship Foundation, 2014-2017 </td> </tr> <tr class="odd views-row-last"> <td class="views-field views-field-counter"> 5. </td> <td class="views-field views-field-field-profiles-honors-awards"> Pew Scholar in the Biomedical Sciences, Pew Charitable Trusts, 2014-2016 </td> </tr> </tbody> </table> </div> </div></div></div></div> </div> </div> <div class="panel-separator"></div><div class="panel-pane pane-views-panes pane-ucsf-person-profile-panel-pane-1" > <h2 class="pane-title">Publications</h2> <div class="pane-content"> <div class="view view-ucsf-person-profile view-id-ucsf_person_profile view-display-id-panel_pane_1 view-dom-id-08c0feab430d3eb1d67b8c47c8cb9432"> <div class="view-content"> <table class="views-table cols-0"> <tbody> <tr class="odd views-row-first"> <td class="views-field views-field-field-person-publications-list"> Bibel B, Raskar T, Couvillion M, Lee M, Kleinman JI, Takeuchi-Tomita N, Churchman LS, Fraser JS, Fujimori DG. Context-specific inhibition of mitochondrial ribosomes by phenicol and oxazolidinone antibiotics. Nucleic Acids Res. 2025 Jan 24; 53(3). </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Liu F, Mailhot O, Glenn IS, Vigneron SF, Bassim V, Xu X, Fonseca-Valencia K, Smith MS, Radchenko DS, Fraser JS, Moroz YS, Irwin JJ, Shoichet BK. The impact of library size and scale of testing on virtual screening. Nat Chem Biol. 2025 Jan 03. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Estevam GO, Linossi EM, Rao J, Macdonald CB, Ravikumar A, Chrispens KM, Capra JA, Coyote-Maestas W, Pimentel H, Collisson EA, Jura N, Fraser JS. Mapping kinase domain resistance mechanisms for the MET receptor tyrosine kinase via deep mutational scanning. bioRxiv. 2024 Dec 05. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Jung H, Kim DH, Díaz RE, White JM, Rucknagel S, Mosby L, Wang Y, Reddy S, Winkler ES, Hassan AO, Ying B, Diamond MS, Locksley RM, Fraser JS, Van Dyken SJ. An ILC2-chitinase circuit restores lung homeostasis after epithelial injury. Sci Immunol. 2024 Oct 18; 9(100):eadl2986. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Flowers J, Echols N, Correy G, Jaishankar P, Togo T, Renslo AR, van den Bedem H, Fraser JS, Wankowicz SA. Expanding Automated Multiconformer Ligand Modeling to Macrocycles and Fragments. bioRxiv. 2024 Sep 23. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Estevam GO, Linossi EM, Macdonald CB, Espinoza CA, Michaud JM, Coyote-Maestas W, Collisson EA, Jura N, Fraser JS. Conserved regulatory motifs in the juxtamembrane domain and kinase N-lobe revealed through deep mutational scanning of the MET receptor tyrosine kinase domain. Elife. 2024 Sep 13; 12. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Gabriella O Estevam, Edmond M Linossi, Christian B Macdonald, Carla A Espinoza, Jennifer M Michaud, Willow Coyote-Maestas, Eric A Collisson, Natalia Jura, James S Fraser. Conserved regulatory motifs in the juxtamembrane domain and kinase N-lobe revealed through deep mutational scanning of the MET receptor tyrosine kinase domain. eLife. 2024 Sep 13; 12. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Suryawanshi RK, Jaishankar P, Correy GJ, Rachman MM, O'Leary PC, Taha TY, Zapatero-Belinchón FJ, McCavittMalvido M, Doruk YU, Stevens MGV, Diolaiti ME, Jogalekar MP, Richards AL, Montano M, Rosecrans J, Matthay M, Togo T, Gonciarz RL, Gopalkrishnan S, Neitz RJ, Krogan NJ, Swaney DL, Shoichet BK, Ott M, Renslo AR, Ashworth A, Fraser JS. The Mac1 ADP-ribosylhydrolase is a Therapeutic Target for SARS-CoV-2. bioRxiv. 2024 Aug 29. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Chen DF, Roe LT, Li Y, Borges AL, Zhang JY, Babbar P, Maji S, Stevens MGV, Correy GJ, Diolaiti ME, Smith DH, Ashworth A, Stroud RM, Kelly MJS, Bondy-Denomy J, Fraser JS. AcrIF11 is a potent CRISPR-specific ADP-ribosyltransferase encoded by phage and plasmid. bioRxiv. 2024 Aug 26. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Correy GJ, Rachman M, Togo T, Gahbauer S, Doruk YU, Stevens M, Jaishankar P, Kelley B, Goldman B, Schmidt M, Kramer T, Ashworth A, Riley P, Shoichet BK, Renslo AR, Walters WP, Fraser JS. Extensive exploration of structure activity relationships for the SARS-CoV-2 macrodomain from shape-based fragment merging and active learning. bioRxiv. 2024 Aug 26. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Trinidad DD, Macdonald CB, Rosenberg OS, Fraser JS, Coyote-Maestas W. Deep mutational scanning of EccD3 reveals the molecular basis of its essentiality in the mycobacterium ESX secretion system. bioRxiv. 2024 Aug 24. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Bibel B, Raskar T, Couvillion M, Lee M, Kleinman JI, Takeuchi-Tomita N, Churchman LS, Fraser JS, Fujimori DG. Context-specific inhibition of mitochondrial ribosomes by phenicol and oxazolidinone antibiotics. bioRxiv. 2024 Aug 21. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Liu F, Mailhot O, Glenn IS, Vigneron SF, Bassim V, Xu X, Fonseca-Valencia K, Smith MS, Radchenko DS, Fraser JS, Moroz YS, Irwin JJ, Shoichet BK. The impact of Library Size and Scale of Testing on Virtual Screening. bioRxiv. 2024 Jul 11. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Wankowicz SA, Fraser JS. Comprehensive encoding of conformational and compositional protein structural ensembles through the mmCIF data structure. IUCrJ. 2024 Jul 01; 11(Pt 4):494-501. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Stephanie A Wankowicz, Ashraya Ravikumar, Shivani Sharma, Blake Riley, Akshay Raju, Daniel W Hogan, Jessica Flowers, Henry van den Bedem, Daniel A Keedy, James S Fraser. Automated multiconformer model building for X-ray crystallography and cryo-EM. eLife. 2024 Jun 21; 12. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Wankowicz SA, Ravikumar A, Sharma S, Riley B, Raju A, Hogan DW, Flowers J, van den Bedem H, Keedy DA, Fraser JS. Automated multiconformer model building for X-ray crystallography and cryo-EM. Elife. 2024 Jun 21; 12. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Díaz RE, Ecker AK, Correy GJ, Asthana P, Young ID, Faust B, Thompson MC, Seiple IB, Van Dyken S, Locksley RM, Fraser JS. Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase. Elife. 2024 Jun 17; 12. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Roberto Efraín Díaz, Andrew K Ecker, Galen J Correy, Pooja Asthana, Iris D Young, Bryan Faust, Michael C Thompson, Ian B Seiple, Steven Van Dyken, Richard M Locksley, James S Fraser. Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase. eLife. 2024 Jun 17; 12. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Rao J, Xin R, Macdonald C, Howard MK, Estevam GO, Yee SW, Wang M, Fraser JS, Coyote-Maestas W, Pimentel H. Rosace: a robust deep mutational scanning analysis framework employing position and mean-variance shrinkage. Genome Biol. 2024 05 24; 25(1):138. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Estevam GO, Linossi EM, Macdonald CB, Espinoza CA, Michaud JM, Coyote-Maestas W, Collisson EA, Jura N, Fraser JS. Conserved regulatory motifs in the juxtamembrane domain and kinase N-lobe revealed through deep mutational scanning of the MET receptor tyrosine kinase domain. bioRxiv. 2024 May 06. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Wankowicz SA, Ravikumar A, Sharma S, Riley BT, Raju A, Flowers J, Hogan D, van den Bedem H, Keedy DA, Fraser JS. Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM. bioRxiv. 2024 Apr 30. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Díaz RE, Ecker AK, Correy GJ, Asthana P, Young ID, Faust B, Thompson MC, Seiple IB, Van Dyken SJ, Locksley RM, Fraser JS. Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase. bioRxiv. 2024 Mar 25. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Avissar-Whiting M, Belliard F, Bertozzi SM, Brand A, Brown K, Clément-Stoneham G, Dawson S, Dey G, Ecer D, Edmunds SC, Farley A, Fischer TD, Franko M, Fraser JS, Funk K, Ganier C, Harrison M, Hatch A, Hazlett H, Hindle S, Hook DW, Hurst P, Kamoun S, Kiley R, Lacy MM, LaFlamme M, Lawrence R, Lemberger T, Leptin M, Lumb E, MacCallum CJ, Marcum CS, Marinello G, Mendonça A, Monaco S, Neves K, Pattinson D, Polka JK, Puebla I, Rittman M, Royle SJ, Saderi D, Sever R, Shearer K, Spiro JE, Stern B, Taraborelli D, Vale R, Vasquez CG, Waltman L, Watt FM, Weinberg ZY, Williams M. Recommendations for accelerating open preprint peer review to improve the culture of science. PLoS Biol. 2024 Feb; 22(2):e3002502. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Varkaris A, Pazolli E, Gunaydin H, Wang Q, Pierce L, Boezio AA, Bulku A, DiPietro L, Fridrich C, Frost A, Giordanetto F, Hamilton EP, Harris K, Holliday M, Hunter TL, Iskandar A, Ji Y, Larivée A, LaRochelle JR, Lescarbeau A, Llambi F, Lormil B, Mader MM, Mar BG, Martin I, McLean TH, Michelsen K, Pechersky Y, Puente-Poushnejad E, Raynor K, Rogala D, Samadani R, Schram AM, Shortsleeves K, Swaminathan S, Tajmir S, Tan G, Tang Y, Valverde R, Wehrenberg B, Wilbur J, Williams BR, Zeng H, Zhang H, Walters WP, Wolf BB, Shaw DE, Bergstrom DA, Watters J, Fraser JS, Fortin PD, Kipp DR. Discovery and Clinical Proof-of-Concept of RLY-2608, a First-in-Class Mutant-Selective Allosteric PI3Kα Inhibitor That Decouples Antitumor Activity from Hyperinsulinemia. Cancer Discov. 2024 Feb 08; 14(2):240-257. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Matthew P. Hancock, James S. Fraser, Andrej Sali. Computing a Bayesian multi-state model of a protein structure from an X-ray diffraction pattern. Biophysical Journal. 2024 Feb 1; 123(3):200a-201a. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Samuel Hoff, Massimiliano Bonomi, James Fraser, Eric Greene. Extracting conformational heterogeneity from 2D and 3D cryo-EM data. Biophysical Journal. 2024 Feb 1; 123(3):50a-51a. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Eric R. Greene, Richard Muniz, Hiroki Yamamura, Samuel Hoff, Angelika Arada, Priyanka Bajaj, Daphne Chen, John D. Lee, Massimiliano Bonomi, Justin M. Kollman, James Fraser. Product-stabilized filamentation by human glutamine synthetase allosterically tunes activity. Biophysical Journal. 2024 Feb 1; 123(3):352a. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Rishav Mitra, James Fraser. Role of conformational dynamics in the catalytic mechanism of viral macrodomains. Biophysical Journal. 2024 Feb 1; 123(3):356a-357a. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Fraser JS, Murcko MA. Structure is beauty, but not always truth. Cell. 2024 Feb 01; 187(3):517-520. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Guérin C, Vinchent A, Fernandes M, Damour I, Laratte A, Tellier R, Estevam GO, Meneboo JP, Villenet C, Descarpentries C, Fraser JS, Figeac M, Cortot AB, Rouleau E, Tulasne D. MET variants with activating N-lobe mutations identified in hereditary papillary renal cell carcinomas still require ligand stimulation. bioRxiv. 2023 Nov 07. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Wolff AM, Nango E, Young ID, Brewster AS, Kubo M, Nomura T, Sugahara M, Owada S, Barad BA, Ito K, Bhowmick A, Carbajo S, Hino T, Holton JM, Im D, O'Riordan LJ, Tanaka T, Tanaka R, Sierra RG, Yumoto F, Tono K, Iwata S, Sauter NK, Fraser JS, Thompson MC. Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography. Nat Chem. 2023 Nov; 15(11):1549-1558. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Kim DH, Wang Y, Jung H, Field RL, Zhang X, Liu TC, Ma C, Fraser JS, Brestoff JR, Van Dyken SJ. A type 2 immune circuit in the stomach controls mammalian adaptation to dietary chitin. Science. 2023 09 08; 381(6662):1092-1098. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Taha TY, Suryawanshi RK, Chen IP, Correy GJ, McCavitt-Malvido M, O'Leary PC, Jogalekar MP, Diolaiti ME, Kimmerly GR, Tsou CL, Gascon R, Montano M, Martinez-Sobrido L, Krogan NJ, Ashworth A, Fraser JS, Ott M. A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication in vivo. PLoS Pathog. 2023 08; 19(8):e1011614. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Sorlin AM, López-Álvarez M, Rabbitt SJ, Alanizi AA, Shuere R, Bobba KN, Blecha J, Sakhamuri S, Evans MJ, Bayles KW, Flavell RR, Rosenberg OS, Sriram R, Desmet T, Nidetzky B, Engel J, Ohliger MA, Fraser JS, Wilson DM. Chemoenzymatic Syntheses of Fluorine-18-Labeled Disaccharides from [18F] FDG Yield Potent Sensors of Living Bacteria In Vivo. J Am Chem Soc. 2023 08 16; 145(32):17632-17642. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Du S, Wankowicz SA, Yabukarski F, Doukov T, Herschlag D, Fraser JS. Refinement of multiconformer ensemble models from multi-temperature X-ray diffraction data. Methods Enzymol. 2023; 688:223-254. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Sorlin AM, López-Álvarez M, Rabbitt SJ, Alanizi AA, Shuere R, Bobba KN, Blecha J, Sakhamuri S, Evans MJ, Bayles KW, Flavell RR, Rosenberg OS, Sriram R, Desmet T, Nidetzky B, Engel J, Ohliger MA, Fraser JS, Wilson DM. Chemoenzymatic syntheses of fluorine-18-labeled disaccharides from [ 18 F]FDG yield potent sensors of living bacteria in vivo. bioRxiv. 2023 May 20. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Taha TY, Suryawanshi RK, Chen IP, Correy GJ, O'Leary PC, Jogalekar MP, McCavitt-Malvido M, Diolaiti ME, Kimmerly GR, Tsou CL, Martinez-Sobrido L, Krogan NJ, Ashworth A, Fraser JS, Ott M. A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication and pathogenesis in vivo. bioRxiv. 2023 May 10. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Du S, Wankowicz SA, Yabukarski F, Doukov T, Herschlag D, Fraser JS. Refinement of Multiconformer Ensemble Models from Multi-temperature X-ray Diffraction Data. bioRxiv. 2023 May 05. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Venkatesan A, Jimenez Castro PD, Morosetti A, Horvath H, Chen R, Redman E, Dunn K, Collins JB, Fraser JS, Andersen EC, Kaplan RM, Gilleard JS. Molecular evidence of widespread benzimidazole drug resistance in Ancylostoma caninum from domestic dogs throughout the USA and discovery of a novel β-tubulin benzimidazole resistance mutation. PLoS Pathog. 2023 03; 19(3):e1011146. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Macdonald CB, Nedrud D, Grimes PR, Trinidad D, Fraser JS, Coyote-Maestas W. DIMPLE: deep insertion, deletion, and missense mutation libraries for exploring protein variation in evolution, disease, and biology. Genome Biol. 2023 02 24; 24(1):36. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Huiting E, Cao X, Ren J, Athukoralage JS, Luo Z, Silas S, An N, Carion H, Zhou Y, Fraser JS, Feng Y, Bondy-Denomy J. Bacteriophages inhibit and evade cGAS-like immune function in bacteria. Cell. 2023 02 16; 186(4):864-876.e21. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Mohamad T. Dandan, James S. Fraser. Context-specific inhibition of translation in mycobacterium. Biophysical Journal. 2023 Feb 1; 122(3):489a. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Eric R. Greene, Richard Muniz, Angelika Arada, D. John Lee, Daphne Chen, Erin Thompson, Hiroki Yamamura, Justin M. Kollman, James Fraser. Reaction coordinate dependent fibrillar formation of human glutamine synthetase tunes activity. Biophysical Journal. 2023 Feb 1; 122(3):474a. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Madani A, Krause B, Greene ER, Subramanian S, Mohr BP, Holton JM, Olmos JL, Xiong C, Sun ZZ, Socher R, Fraser JS, Naik N. Large language models generate functional protein sequences across diverse families. Nat Biotechnol. 2023 08; 41(8):1099-1106. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Gahbauer S, Correy GJ, Schuller M, Ferla MP, Doruk YU, Rachman M, Wu T, Diolaiti M, Wang S, Neitz RJ, Fearon D, Radchenko DS, Moroz YS, Irwin JJ, Renslo AR, Taylor JC, Gestwicki JE, von Delft F, Ashworth A, Ahel I, Shoichet BK, Fraser JS. Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2. Proc Natl Acad Sci U S A. 2023 01 10; 120(2):e2212931120. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Wych DC, Aoto PC, Vu L, Wolff AM, Mobley DL, Fraser JS, Taylor SS, Wall ME. Molecular-dynamics simulation methods for macromolecular crystallography. Acta Crystallogr D Struct Biol. 2023 Jan 01; 79(Pt 1):50-65. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Michaud JM, Madani A, Fraser JS. A language model beats alphafold2 on orphans. Nat Biotechnol. 2022 11; 40(11):1576-1577. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Yabukarski F, Doukov T, Pinney MM, Biel JT, Fraser JS, Herschlag D. Ensemble-function relationships to dissect mechanisms of enzyme catalysis. 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Curr Opin Struct Biol. 2018 06; 50:109-116. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Thomaston JL, Woldeyes RA, Nakane T, Yamashita A, Tanaka T, Koiwai K, Brewster AS, Barad BA, Chen Y, Lemmin T, Uervirojnangkoorn M, Arima T, Kobayashi J, Masuda T, Suzuki M, Sugahara M, Sauter NK, Tanaka R, Nureki O, Tono K, Joti Y, Nango E, Iwata S, Yumoto F, Fraser JS, DeGrado WF. XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction. Proc Natl Acad Sci U S A. 2017 12 19; 114(51):13357-13362. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Acker TM, Gable JE, Bohn MF, Jaishankar P, Thompson MC, Fraser JS, Renslo AR, Craik CS. Allosteric Inhibitors, Crystallography, and Comparative Analysis Reveal Network of Coordinated Movement across Human Herpesvirus Proteases. J Am Chem Soc. 2017 08 30; 139(34):11650-11653. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Offenbacher AR, Hu S, Poss EM, Carr CAM, Scouras AD, Prigozhin DM, Iavarone AT, Palla A, Alber T, Fraser JS, Klinman JP. Hydrogen-Deuterium Exchange of Lipoxygenase Uncovers a Relationship between Distal, Solvent Exposed Protein Motions and the Thermal Activation Barrier for Catalytic Proton-Coupled Electron Tunneling. ACS Cent Sci. 2017 Jun 28; 3(6):570-579. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Biel JT, Thompson MC, Cunningham CN, Corn JE, Fraser JS. Flexibility and Design: Conformational Heterogeneity along the Evolutionary Trajectory of a Redesigned Ubiquitin. Structure. 2017 05 02; 25(5):739-749.e3. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Adolph MB, Ara A, Feng Y, Wittkopp CJ, Emerman M, Fraser JS, Chelico L. Cytidine deaminase efficiency of the lentiviral viral restriction factor APOBEC3C correlates with dimerization. Nucleic Acids Res. 2017 04 07; 45(6):3378-3394. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Russi S, González A, Kenner LR, Keedy DA, Fraser JS, van den Bedem H. Conformational variation of proteins at room temperature is not dominated by radiation damage. J Synchrotron Radiat. 2017 01 01; 24(Pt 1):73-82. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Wang RY, Song Y, Barad BA, Cheng Y, Fraser JS, DiMaio F. Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta. Elife. 2016 09 26; 5. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Urzhumtsev A, Afonine PV, Van Benschoten AH, Fraser JS, Adams PD. From deep TLS validation to ensembles of atomic models built from elemental motions. Addenda and corrigendum. Acta Crystallogr D Struct Biol. 2016 09 01; 72(Pt 9):1073-1075. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Berg JM, Bhalla N, Bourne PE, Chalfie M, Drubin DG, Fraser JS, Greider CW, Hendricks M, Jones C, Kiley R, King S, Kirschner MW, Krumholz HM, Lehmann R, Leptin M, Pulverer B, Rosenzweig B, Spiro JE, Stebbins M, Strasser C, Swaminathan S, Turner P, Vale RD, VijayRaghavan K, Wolberger C. SCIENTIFIC COMMUNITY. Preprints for the life sciences. Science. 2016 May 20; 352(6288):899-901. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Mavor D, Barlow K, Thompson S, Barad BA, Bonny AR, Cario CL, Gaskins G, Liu Z, Deming L, Axen SD, Caceres E, Chen W, Cuesta A, Gate RE, Green EM, Hulce KR, Ji W, Kenner LR, Mensa B, Morinishi LS, Moss SM, Mravic M, Muir RK, Niekamp S, Nnadi CI, Palovcak E, Poss EM, Ross TD, Salcedo EC, See SK, Subramaniam M, Wong AW, Li J, Thorn KS, Conchúir SÓ, Roscoe BP, Chow ED, DeRisi JL, Kortemme T, Bolon DN, Fraser JS. Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting. Elife. 2016 04 25; 5. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Van Benschoten AH, Liu L, Gonzalez A, Brewster AS, Sauter NK, Fraser JS, Wall ME. Measuring and modeling diffuse scattering in protein X-ray crystallography. Proc Natl Acad Sci U S A. 2016 Apr 12; 113(15):4069-74. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Meyer PA, Socias S, Key J, Ransey E, Tjon EC, Buschiazzo A, Lei M, Botka C, Withrow J, Neau D, Rajashankar K, Anderson KS, Baxter RH, Blacklow SC, Boggon TJ, Bonvin AM, Borek D, Brett TJ, Caflisch A, Chang CI, Chazin WJ, Corbett KD, Cosgrove MS, Crosson S, Dhe-Paganon S, Di Cera E, Drennan CL, Eck MJ, Eichman BF, Fan QR, Ferré-D'Amaré AR, Fromme JC, Garcia KC, Gaudet R, Gong P, Harrison SC, Heldwein EE, Jia Z, Keenan RJ, Kruse AC, Kvansakul M, McLellan JS, Modis Y, Nam Y, Otwinowski Z, Pai EF, Pereira PJ, Petosa C, Raman CS, Rapoport TA, Roll-Mecak A, Rosen MK, Rudenko G, Schlessinger J, Schwartz TU, Shamoo Y, Sondermann H, Tao YJ, Tolia NH, Tsodikov OV, Westover KD, Wu H, Foster I, Fraser JS, Maia FR, Gonen T, Kirchhausen T, Diederichs K, Crosas M, Sliz P. Data publication with the structural biology data grid supports live analysis. Nat Commun. 2016 Mar 07; 7:10882. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Cimermancic P, Weinkam P, Rettenmaier TJ, Bichmann L, Keedy DA, Woldeyes RA, Schneidman-Duhovny D, Demerdash ON, Mitchell JC, Wells JA, Fraser JS, Sali A. CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites. J Mol Biol. 2016 Feb 22; 428(4):709-719. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Baxter EL, Aguila L, Alonso-Mori R, Barnes CO, Bonagura CA, Brehmer W, Brunger AT, Calero G, Caradoc-Davies TT, Chatterjee R, Degrado WF, Fraser JS, Ibrahim M, Kern J, Kobilka BK, Kruse AC, Larsson KM, Lemke HT, Lyubimov AY, Manglik A, McPhillips SE, Norgren E, Pang SS, Soltis SM, Song J, Thomaston J, Tsai Y, Weis WI, Woldeyes RA, Yachandra V, Yano J, Zouni A, Cohen AE. High-density grids for efficient data collection from multiple crystals. Acta Crystallogr D Struct Biol. 2016 Jan; 72(Pt 1):2-11. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Thomaston JL, Alfonso-Prieto M, Woldeyes RA, Fraser JS, Klein ML, Fiorin G, DeGrado WF. High-resolution structures of the M2 channel from influenza A virus reveal dynamic pathways for proton stabilization and transduction. Proc Natl Acad Sci U S A. 2015 Nov 17; 112(46):14260-5. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Keedy DA, Fraser JS, van den Bedem H. Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit. PLoS Comput Biol. 2015 Oct; 11(10):e1004507. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Keedy DA, Kenner LR, Warkentin M, Woldeyes RA, Hopkins JB, Thompson MC, Brewster AS, Van Benschoten AH, Baxter EL, Uervirojnangkoorn M, McPhillips SE, Song J, Alonso-Mori R, Holton JM, Weis WI, Brunger AT, Soltis SM, Lemke H, Gonzalez A, Sauter NK, Cohen AE, van den Bedem H, Thorne RE, Fraser JS. Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography. Elife. 2015 Sep 30; 4. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Barad BA, Echols N, Wang RY, Cheng Y, DiMaio F, Adams PD, Fraser JS. EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy. Nat Methods. 2015 Oct; 12(10):943-6. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Urzhumtsev A, Afonine PV, Van Benschoten AH, Fraser JS, Adams PD. From deep TLS validation to ensembles of atomic models built from elemental motions. Acta Crystallogr D Biol Crystallogr. 2015 Aug; 71(Pt 8):1668-83. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Van Benschoten AH, Afonine PV, Terwilliger TC, Wall ME, Jackson CJ, Sauter NK, Adams PD, Urzhumtsev A, Fraser JS. Predicting X-ray diffuse scattering from translation-libration-screw structural ensembles. Acta Crystallogr D Biol Crystallogr. 2015 Aug; 71(Pt 8):1657-67. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Fischer M, Shoichet BK, Fraser JS. One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites. Chembiochem. 2015 Jul 27; 16(11):1560-4. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Dellus-Gur E, Elias M, Caselli E, Prati F, Salverda ML, de Visser JA, Fraser JS, Tawfik DS. Negative Epistasis and Evolvability in TEM-1 β-Lactamase--The Thin Line between an Enzyme's Conformational Freedom and Disorder. J Mol Biol. 2015 Jul 17; 427(14):2396-409. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Kane JR, Stanley DJ, Hultquist JF, Johnson JR, Mietrach N, Binning JM, Jónsson SR, Barelier S, Newton BW, Johnson TL, Franks-Skiba KE, Li M, Brown WL, Gunnarsson HI, Adalbjornsdóttir A, Fraser JS, Harris RS, Andrésdóttir V, Gross JD, Krogan NJ. Lineage-Specific Viral Hijacking of Non-canonical E3 Ubiquitin Ligase Cofactors in the Evolution of Vif Anti-APOBEC3 Activity. Cell Rep. 2015 May 26; 11(8):1236-50. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> van den Bedem H, Fraser JS. Integrative, dynamic structural biology at atomic resolution--it's about time. Nat Methods. 2015 Apr; 12(4):307-18. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Bhabha G, Biel JT, Fraser JS. Keep on moving: discovering and perturbing the conformational dynamics of enzymes. Acc Chem Res. 2015 Feb 17; 48(2):423-30. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Wall ME, Van Benschoten AH, Sauter NK, Adams PD, Fraser JS, Terwilliger TC. Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering. Proc Natl Acad Sci U S A. 2014 Dec 16; 111(50):17887-92. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Williams BB, Van Benschoten AH, Cimermancic P, Donia MS, Zimmermann M, Taketani M, Ishihara A, Kashyap PC, Fraser JS, Fischbach MA. Discovery and characterization of gut microbiota decarboxylases that can produce the neurotransmitter tryptamine. Cell Host Microbe. 2014 Oct 08; 16(4):495-503. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Woldeyes RA, Sivak DA, Fraser JS. E pluribus unum, no more: from one crystal, many conformations. Curr Opin Struct Biol. 2014 Oct; 28:56-62. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Keedy DA, van den Bedem H, Sivak DA, Petsko GA, Ringe D, Wilson MA, Fraser JS. Crystal cryocooling distorts conformational heterogeneity in a model Michaelis complex of DHFR. Structure. 2014 Jun 10; 22(6):899-910. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Fischer M, Coleman RG, Fraser JS, Shoichet BK. Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery. Nat Chem. 2014 Jul; 6(7):575-83. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Wall ME, Adams PD, Fraser JS, Sauter NK. Diffuse X-ray scattering to model protein motions. Structure. 2014 Feb 04; 22(2):182-4. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Fenwick RB, van den Bedem H, Fraser JS, Wright PE. Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR. Proc Natl Acad Sci U S A. 2014 Jan 28; 111(4):E445-54. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Lang PT, Holton JM, Fraser JS, Alber T. Protein structural ensembles are revealed by redefining X-ray electron density noise. Proc Natl Acad Sci U S A. 2014 Jan 07; 111(1):237-42. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Braberg H, Jin H, Moehle EA, Chan YA, Wang S, Shales M, Benschop JJ, Morris JH, Qiu C, Hu F, Tang LK, Fraser JS, Holstege FC, Hieter P, Guthrie C, Kaplan CD, Krogan NJ. From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II. Cell. 2013 Aug 15; 154(4):775-88. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> van den Bedem H, Bhabha G, Yang K, Wright PE, Fraser JS. Automated identification of functional dynamic contact networks from X-ray crystallography. Nat Methods. 2013 Sep; 10(9):896-902. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Fraser JS, Gross JD, Krogan NJ. From systems to structure: bridging networks and mechanism. Mol Cell. 2013 Jan 24; 49(2):222-31. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Ollikainen N, Smith CA, Fraser JS, Kortemme T. Flexible backbone sampling methods to model and design protein alternative conformations. Methods Enzymol. 2013; 523:61-85. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Vila JA, Sue SC, Fraser JS, Scheraga HA, Dyson HJ. CheShift-2 resolves a local inconsistency between two X-ray crystal structures. J Biomol NMR. 2012 Oct; 54(2):193-8. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Beltrao P, Albanèse V, Kenner LR, Swaney DL, Burlingame A, Villén J, Lim WA, Fraser JS, Frydman J, Krogan NJ. Systematic functional prioritization of protein posttranslational modifications. Cell. 2012 Jul 20; 150(2):413-25. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Kapp GT, Liu S, Stein A, Wong DT, Reményi A, Yeh BJ, Fraser JS, Taunton J, Lim WA, Kortemme T. Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair. Proc Natl Acad Sci U S A. 2012 Apr 03; 109(14):5277-82. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Fraser JS, van den Bedem H, Samelson AJ, Lang PT, Holton JM, Echols N, Alber T. Accessing protein conformational ensembles using room-temperature X-ray crystallography. Proc Natl Acad Sci U S A. 2011 Sep 27; 108(39):16247-52. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Fraser JS, Jackson CJ. Mining electron density for functionally relevant protein polysterism in crystal structures. Cell Mol Life Sci. 2011 Jun; 68(11):1829-41. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Maghzal N, Vogt E, Reintsch W, Fraser JS, Fagotto F. The tumor-associated EpCAM regulates morphogenetic movements through intracellular signaling. J Cell Biol. 2010 Nov 01; 191(3):645-59. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Lang PT, Ng HL, Fraser JS, Corn JE, Echols N, Sales M, Holton JM, Alber T. Automated electron-density sampling reveals widespread conformational polymorphism in proteins. Protein Sci. 2010 Jul; 19(7):1420-31. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Fraser JS, Clarkson MW, Degnan SC, Erion R, Kern D, Alber T. Hidden alternative structures of proline isomerase essential for catalysis. Nature. 2009 Dec 03; 462(7273):669-73. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Fraser JS, Maxwell KL, Davidson AR. Immunoglobulin-like domains on bacteriophage: weapons of modest damage? Curr Opin Microbiol. 2007 Aug; 10(4):382-7. </td> </tr> <tr class="odd"> <td class="views-field views-field-field-person-publications-list"> Fraser JS, Merlie JP, Echols N, Weisfield SR, Mignot T, Wemmer DE, Zusman DR, Alber T. An atypical receiver domain controls the dynamic polar localization of the Myxococcus xanthus social motility protein FrzS. Mol Microbiol. 2007 Jul; 65(2):319-32. </td> </tr> <tr class="even"> <td class="views-field views-field-field-person-publications-list"> Fraser JS, Yu Z, Maxwell KL, Davidson AR. Ig-like domains on bacteriophages: a tale of promiscuity and deceit. J Mol Biol. 2006 Jun 02; 359(2):496-507. </td> </tr> <tr class="odd views-row-last"> <td class="views-field views-field-field-person-publications-list"> Womack S, Compton WM, Dennis M, McCormick S, Fraser J, Horton JC, Spitznagel EL, Cottler LB. Improving treatment services for substance abusers with comorbid depression. Am J Addict. 2004 May-Jun; 13(3):295-304. </td> </tr> </tbody> </table> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div>  </div>  </div>  </div>  </div>  <div role="complementary" class="footer-make-a-gift-and-quote"> <div class="footer-make-a-gift"> <a href="https://makeagift.ucsf.edu/site/SPageServer?pagename=A1_API_GeneralGivingForm&Primary=Pharmacy">Make a gift</a> </div> <div class="footer-quote"> Science is the foundation of the School of Pharmacy’s pioneering research, individualized patient care, and unparalleled PharmD and PhD education programs. </div> </div> <div class="footer-wrapper-outer" role="contentinfo"> <div class="footer-wrapper-inner"> <div class="footer-site-names-and-disclaimer"> </div> <div class="footer menu"> <ul id="footer-menu" class="links clearfix footer-menu"><li class="0 first"><a href="https://pharmacy.ucsf.edu/news/submit/?source=footer" title="" aria-label="Submit news via the Newsletter and Social Media Submission Form">Submit news</a></li> <li class="1"><a href="https://pharmacy.ucsf.edu/suggestions" title="">Suggestions</a></li> <li class="2"><a href="https://pharmacy.ucsf.edu/support?reporturl=https%3A//pharmacy.ucsf.edu/james-fraser" title="">Report a problem</a></li> <li class="menu-18196"><a href="/about/contact" title="">Contact us</a></li> <li class="menu-91601"><a href="https://websites.ucsf.edu/digital-accessibility" title="">Accessibility</a></li> <li class="menu-91606"><a href="https://www.ucsf.edu/website-privacy-policy" title="">Privacy policy</a></li> <li class="menu-91611"><a href="https://websites.ucsf.edu/website-terms-use" title="">Terms of use</a></li> <li class="menu-91616"><a href="https://websites.ucsf.edu/azlist" title="">A-Z website list</a></li> <li class="menu-7861 last"><a href="/saml_login?destination=james-fraser" title="" rel="nofollow">Log in</a></li> </ul> </div> <div class="footer-social"> <div class="item-list"><ul><li class="first"><a href="https://www.facebook.com/ucsfpharmacy" class="facebook">Facebook</a></li> <li><a href="https://www.youtube.com/@ucsfpharmacy" class="youtube">YouTube</a></li> <li><a href="https://www.linkedin.com/showcase/ucsf-school-of-pharmacy" class="linkedin">LinkedIn</a></li> <li class="last"><a href="https://www.instagram.com/ucsfpharmacy/" class="instagram">Instagram</a></li> </ul></div> </div> <div class="copyright"> © 2002–2025 The Regents of the University of California </div> </div> </div> <script data-cfasync="false" src="/cdn-cgi/scripts/5c5dd728/cloudflare-static/email-decode.min.js"></script><script type="text/javascript" src="/sites/pharmacy.ucsf.edu/files/advagg_js/js__GM3GJPR36rRIz0TRkjC5OQwrioSyN9aoYRivDhCO_AM__qAl84FcCv2jyN22yFGS5Oc85cjd9zKX6p_cFNLGhe-M__seqvHfaz3fVlgbfb4sGxYkGyco2BfGnhCPlf7TXVcuY.js" async="async"></script> <script type="text/javascript" src="/sites/pharmacy.ucsf.edu/files/advagg_js/js__BXT3KPF6ph4oEqAPjWiNmzlSjlQ9cW6B36GuZ8Knzt8__kNEvQrCieBaWSkG2Yi7cvf5o5n825wJD1XixHxWBUFo__seqvHfaz3fVlgbfb4sGxYkGyco2BfGnhCPlf7TXVcuY.js"></script> <script type="text/javascript">window.NREUM||(NREUM={});NREUM.info={"beacon":"bam.nr-data.net","licenseKey":"3132ed34d6","applicationID":"70694569","transactionName":"YFRUNUpZDUdUUEddV1kedRRLTAxZGkNSU11oXFcPWV8GRmpdXFBdaEdfBE9nE1VSVhxBW0RXaRFdShBbWw==","queueTime":14,"applicationTime":895,"atts":"TBNXQwJDHkk=","errorBeacon":"bam.nr-data.net","agent":""}</script></body> </html>

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