James Fraser, PhD

Title(s)Professor, Bioengineering
SchoolSchool of Pharmacy
AddressLocation Required, #001
Phone415-493-8421
Pronounshe/him/his
ORCID ORCID Icon0000-0002-5080-2859 Additional info
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    Collapse Biography 
    Collapse Education and Training
    McGill UniversityB.Sc.2005Biology
    University of California BerkeleyPh.D.2010Molecular and Cell Biology
    University of California, San Francisco, CA2019Diversity, Equity, and Inclusion Champion Training
    Collapse Awards and Honors
    Pew Charitable Trusts 2014  - 2016Pew Scholar in the Biomedical Sciences
    Kinship Foundation2014  - 2017Searle Scholar
    The David and Lucille Packard Foundation2014  - 2019Packard Fellow
    International Union of Crystallography2020W.H. and W.L. Bragg Prize
    UCSF2020Byers Award in Basic Science

    Collapse Overview 
    Collapse Overview
    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.

    Collapse Research 
    Collapse Research Activities and Funding
    Resolving ensemble averaged conformations by multi-temperature x-ray crystallography
    NIH R01GM123159Jan 1, 2018 - Dec 31, 2021
    Role: Principal Investigator
    Model Comparison in Structural Biology
    NIH R21GM110580Apr 1, 2014 - Mar 31, 2017
    Role: Principal Investigator
    The Impact of Mutation on the Conformations and Recognition of Ubiquitin
    NIH DP5OD009180Sep 20, 2011 - Aug 31, 2017
    Role: Principal Investigator

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    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase. bioRxiv. 2024 Mar 25. Díaz RE, Ecker AK, Correy GJ, Asthana P, Young ID, Faust B, Thompson MC, Seiple IB, Van Dyken SJ, Locksley RM, Fraser JS. PMID: 37398339; PMCID: PMC10312649.
      View in: PubMed   Mentions:
    2. Recommendations for accelerating open preprint peer review to improve the culture of science. PLoS Biol. 2024 Feb; 22(2):e3002502. 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. PMID: 38421949; PMCID: PMC10903809.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    3. 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. 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. PMID: 37916956; PMCID: PMC10850943.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    4. Structure is beauty, but not always truth. Cell. 2024 Feb 01; 187(3):517-520. Fraser JS, Murcko MA. PMID: 38306978; PMCID: PMC10947451.
      View in: PubMed   Mentions:    Fields:    
    5. Extracting conformational heterogeneity from 2D and 3D cryo-EM data. Biophysical Journal. 2024 Feb 1; 123(3):50a-51a. Hoff HS, Bonomi BM, Fraser FJ, Greene GE. .
      View in: Publisher Site   Mentions:
    6. 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. Hancock HM, Fraser FJ, Sali SA. .
      View in: Publisher Site   Mentions:
    7. Product-stabilized filamentation by human glutamine synthetase allosterically tunes activity. Biophysical Journal. 2024 Feb 1; 123(3):352a. Greene GE, Muniz MR, Yamamura YH, Hoff HS, Arada AA, Bajaj BP, Chen CD, Lee LJ, Bonomi BM, Kollman KJ, Fraser FJ. .
      View in: Publisher Site   Mentions:
    8. Role of conformational dynamics in the catalytic mechanism of viral macrodomains. Biophysical Journal. 2024 Feb 1; 123(3):356a-357a. Mitra MR, Fraser FJ. .
      View in: Publisher Site   Mentions:
    9. MET variants with activating N-lobe mutations identified in hereditary papillary renal cell carcinomas still require ligand stimulation. bioRxiv. 2023 Nov 07. 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. PMID: 37965202; PMCID: PMC10635098.
      View in: PubMed   Mentions:
    10. Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography. Nat Chem. 2023 Nov; 15(11):1549-1558. 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. PMID: 37723259; PMCID: PMC10624634.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    11. A type 2 immune circuit in the stomach controls mammalian adaptation to dietary chitin. Science. 2023 09 08; 381(6662):1092-1098. Kim DH, Wang Y, Jung H, Field RL, Zhang X, Liu TC, Ma C, Fraser JS, Brestoff JR, Van Dyken SJ. PMID: 37676935; PMCID: PMC10865997.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    12. 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. 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. PMID: 37651466; PMCID: PMC10499221.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    13. Conserved regulatory motifs in the juxtamembrane domain and kinase N-lobe revealed through deep mutational scanning of the MET receptor tyrosine kinase domain. bioRxiv. 2023 Aug 03. Estevam GO, Linossi EM, Macdonald CB, Espinoza CA, Michaud JM, Coyote-Maestas W, Collisson EA, Jura N, Fraser JS. PMID: 37577651; PMCID: PMC10418267.
      View in: PubMed   Mentions:
    14. 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. 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. PMID: 37535945; PMCID: PMC10436271.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    15. Refinement of multiconformer ensemble models from multi-temperature X-ray diffraction data. Methods Enzymol. 2023; 688:223-254. Du S, Wankowicz SA, Yabukarski F, Doukov T, Herschlag D, Fraser JS. PMID: 37748828; PMCID: PMC10637719.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    16. Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM. bioRxiv. 2023 Jun 29. Wankowicz SA, Ravikumar A, Sharma S, Riley BT, Raju A, Hogan DW, van den Bedem H, Keedy DA, Fraser JS. PMID: 37425870; PMCID: PMC10327213.
      View in: PubMed   Mentions:
    17. Chemoenzymatic syntheses of fluorine-18-labeled disaccharides from [ 18 F]FDG yield potent sensors of living bacteria in vivo. bioRxiv. 2023 May 20. 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. PMID: 37293043; PMCID: PMC10245702.
      View in: PubMed   Mentions:
    18. 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. 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. PMID: 37131711; PMCID: PMC10153184.
      View in: PubMed   Mentions:
    19. Refinement of Multiconformer Ensemble Models from Multi-temperature X-ray Diffraction Data. bioRxiv. 2023 May 05. Du S, Wankowicz SA, Yabukarski F, Doukov T, Herschlag D, Fraser JS. PMID: 37205593; PMCID: PMC10187334.
      View in: PubMed   Mentions:
    20. 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. 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. PMID: 36862759; PMCID: PMC10013918.
      View in: PubMed   Mentions: 3     Fields:    Translation:Animals
    21. 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. Macdonald CB, Nedrud D, Grimes PR, Trinidad D, Fraser JS, Coyote-Maestas W. PMID: 36829241; PMCID: PMC9951526.
      View in: PubMed   Mentions: 6     Fields:    
    22. Bacteriophages inhibit and evade cGAS-like immune function in bacteria. Cell. 2023 02 16; 186(4):864-876.e21. 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. PMID: 36750095; PMCID: PMC9975087.
      View in: PubMed   Mentions: 18     Fields:    Translation:AnimalsCells
    23. Reaction coordinate dependent fibrillar formation of human glutamine synthetase tunes activity. Biophysical Journal. 2023 Feb 1; 122(3):474a. Greene GE, Muniz MR, Arada AA, Lee LD, Chen CD, Thompson TE, Yamamura YH, Kollman KJ, Fraser FJ. .
      View in: Publisher Site   Mentions:
    24. Context-specific inhibition of translation in mycobacterium. Biophysical Journal. 2023 Feb 1; 122(3):489a. Dandan DM, Fraser FJ. .
      View in: Publisher Site   Mentions:
    25. Large language models generate functional protein sequences across diverse families. Nat Biotechnol. 2023 08; 41(8):1099-1106. Madani A, Krause B, Greene ER, Subramanian S, Mohr BP, Holton JM, Olmos JL, Xiong C, Sun ZZ, Socher R, Fraser JS, Naik N. PMID: 36702895; PMCID: PMC10400306.
      View in: PubMed   Mentions: 77     Fields:    Translation:Cells
    26. 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. 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. PMID: 36598939; PMCID: PMC9926234.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCellsPHPublic Health
    27. Molecular-dynamics simulation methods for macromolecular crystallography. Acta Crystallogr D Struct Biol. 2023 Jan 01; 79(Pt 1):50-65. Wych DC, Aoto PC, Vu L, Wolff AM, Mobley DL, Fraser JS, Taylor SS, Wall ME. PMID: 36601807; PMCID: PMC9815100.
      View in: PubMed   Mentions: 5  Translation:Cells
    28. A language model beats alphafold2 on orphans. Nat Biotechnol. 2022 11; 40(11):1576-1577. Michaud JM, Madani A, Fraser JS. PMID: 36192635; PMCID: PMC9669189.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    29. Ensemble-function relationships to dissect mechanisms of enzyme catalysis. Sci Adv. 2022 10 14; 8(41):eabn7738. Yabukarski F, Doukov T, Pinney MM, Biel JT, Fraser JS, Herschlag D. PMID: 36240280; PMCID: PMC9565801.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    30. Of problems and opportunities-How to treat and how to not treat crystallographic fragment screening data. Protein Sci. 2022 09; 31(9):e4391. Weiss MS, Wollenhaupt J, Correy GJ, Fraser JS, Heine A, Klebe G, Krojer T, Thunissen M, Pearce NM. PMID: 36040268; PMCID: PMC9424839.
      View in: PubMed   Mentions: 3     Fields:    
    31. Innate type 2 immunity controls hair follicle commensalism by Demodex mites. Immunity. 2022 10 11; 55(10):1891-1908.e12. Ricardo-Gonzalez RR, Kotas ME, O'Leary CE, Singh K, Damsky W, Liao C, Arouge E, Tenvooren I, Marquez DM, Schroeder AW, Cohen JN, Fassett MS, Lee J, Daniel SG, Bittinger K, Díaz RE, Fraser JS, Ali N, Ansel KM, Spitzer MH, Liang HE, Locksley RM. PMID: 36044899; PMCID: PMC9561030.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    32. The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature. Sci Adv. 2022 May 27; 8(21):eabo5083. Correy GJ, Kneller DW, Phillips G, Pant S, Russi S, Cohen AE, Meigs G, Holton JM, Gahbauer S, Thompson MC, Ashworth A, Coates L, Kovalevsky A, Meilleur F, Fraser JS. PMID: 35622909; PMCID: PMC9140965.
      View in: PubMed   Mentions: 14     Fields:    
    33. Innate type 2 immunity controls hair follicle commensalism by Demodex mites. The Journal of Immunology. 2022 May 1; 208(1_Supplement):50.39-50.39. Ricardo-Gonzalez RR, Kotas KM, O’Leary OC, Tenvooren TI, Marquez MD, Singh SK, Damsky DW, Liao LC, Schroeder SA, Cohen CJ, Fassett FM, Lee LJ, Daniel DS, Bittinger BK, Diaz DR, Fraser FJ, Ansel AK, Spitzer SM, Liang LH, Locksley LR. .
      View in: Publisher Site   Mentions:
    34. Ligand binding remodels protein side-chain conformational heterogeneity. Elife. 2022 03 21; 11. Wankowicz SA, de Oliveira SH, Hogan DW, van den Bedem H, Fraser JS. PMID: 35312477; PMCID: PMC9084896.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    35. Accurate positioning of functional residues with robotics-inspired computational protein design. Proc Natl Acad Sci U S A. 2022 03 15; 119(11):e2115480119. Krivacic C, Kundert K, Pan X, Pache RA, Liu L, Conchúir SO, Jeliazkov JR, Gray JJ, Thompson MC, Fraser JS, Kortemme T. PMID: 35254891; PMCID: PMC8931229.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    36. Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics. Nat Struct Mol Biol. 2022 02; 29(2):162-171. Tsai K, Stojkovic V, Lee DJ, Young ID, Szal T, Klepacki D, Vázquez-Laslop N, Mankin AS, Fraser JS, Fujimori DG. PMID: 35165456; PMCID: PMC8906282.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    37. Integration of software tools for integrative modeling of biomolecular systems. J Struct Biol. 2022 03; 214(1):107841. Hancock M, Peulen TO, Webb B, Poon B, Fraser JS, Adams P, Sali A. PMID: 35149213; PMCID: PMC9278553.
      View in: PubMed   Mentions: 1     Fields:    
    38. Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance. Elife. 2022 01 11; 11. Tsai K, Stojkovic V, Noda-Garcia L, Young ID, Myasnikov AG, Kleinman J, Palla A, Floor SN, Frost A, Fraser JS, Tawfik DS, Fujimori DG. PMID: 35015630; PMCID: PMC8752094.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    39. A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis. Nat Chem Biol. 2022 02; 18(2):161-170. Jayaraman V, Lee DJ, Elad N, Vimer S, Sharon M, Fraser JS, Tawfik DS. PMID: 34931064; PMCID: PMC8810680.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    40. CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes. Res Sq. 2021 May 19. Gupta M, Azumaya CM, Moritz M, Pourmal S, Diallo A, Merz GE, Jang G, Bouhaddou M, Fossati A, Brilot AF, Diwanji D, Hernandez E, Herrera N, Kratochvil HT, Lam VL, Li F, Li Y, Nguyen HC, Nowotny C, Owens TW, Peters JK, Rizo AN, Schulze-Gahmen U, Smith AM, Young ID, Yu Z, Asarnow D, Billesbølle C, Campbell MG, Chen J, Chen KH, Chio US, Dickinson MS, Doan L, Jin M, Kim K, Li J, Li YL, Linossi E, Liu Y, Lo M, Lopez J, Lopez KE, Mancino A, Moss FR, Paul MD, Pawar KI, Pelin A, Pospiech TH, Puchades C, Remesh SG, Safari M, Schaefer K, Sun M, Tabios MC, Thwin AC, Titus EW, Trenker R, Tse E, Tsui TKM, Wang F, Zhang K, Zhang Y, Zhao J, Zhou F, Zhou Y, Zuliani-Alvarez L, QCRG Structural Biology Consortium, Agard DA, Cheng Y, Fraser JS, Jura N, Kortemme T, Manglik A, Southworth DR, Stroud RM, Swaney DL, Krogan NJ, Frost A, Rosenberg OS, Verba KA. PMID: 34031651; PMCID: PMC8142659.
      View in: PubMed   Mentions: 1  
    41. State of the structure address on MET receptor activation by HGF. Biochem Soc Trans. 2021 04 30; 49(2):645-661. Linossi EM, Estevam GO, Oshima M, Fraser JS, Collisson EA, Jura N. PMID: 33860789; PMCID: PMC8711257.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    42. ORACLE reveals a bright future to fight bacteria. Elife. 2021 04 15; 10. Coyote-Maestas W, Fraser JS. PMID: 33856343; PMCID: PMC8049741.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    43. Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking. Sci Adv. 2021 04; 7(16). Schuller M, Correy GJ, Gahbauer S, Fearon D, Wu T, Díaz RE, Young ID, Carvalho Martins L, Smith DH, Schulze-Gahmen U, Owens TW, Deshpande I, Merz GE, Thwin AC, Biel JT, Peters JK, Moritz M, Herrera N, Kratochvil HT, QCRG Structural Biology Consortium, Aimon A, Bennett JM, Brandao Neto J, Cohen AE, Dias A, Douangamath A, Dunnett L, Fedorov O, Ferla MP, Fuchs MR, Gorrie-Stone TJ, Holton JM, Johnson MG, Krojer T, Meigs G, Powell AJ, Rack JGM, Rangel VL, Russi S, Skyner RE, Smith CA, Soares AS, Wierman JL, Zhu K, O'Brien P, Jura N, Ashworth A, Irwin JJ, Thompson MC, Gestwicki JE, von Delft F, Shoichet BK, Fraser JS, Ahel I. PMID: 33853786; PMCID: PMC8046379.
      View in: PubMed   Mentions: 62     Fields:    Translation:HumansCells
    44. Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge. Nat Methods. 2021 02; 18(2):156-164. Lawson CL, Kryshtafovych A, Adams PD, Afonine PV, Baker ML, Barad BA, Bond P, Burnley T, Cao R, Cheng J, Chojnowski G, Cowtan K, Dill KA, DiMaio F, Farrell DP, Fraser JS, Herzik MA, Hoh SW, Hou J, Hung LW, Igaev M, Joseph AP, Kihara D, Kumar D, Mittal S, Monastyrskyy B, Olek M, Palmer CM, Patwardhan A, Perez A, Pfab J, Pintilie GD, Richardson JS, Rosenthal PB, Sarkar D, Schäfer LU, Schmid MF, Schröder GF, Shekhar M, Si D, Singharoy A, Terashi G, Terwilliger TC, Vaiana A, Wang L, Wang Z, Wankowicz SA, Williams CJ, Winn M, Wu T, Yu X, Zhang K, Berman HM, Chiu W. PMID: 33542514; PMCID: PMC7864804.
      View in: PubMed   Mentions: 34     Fields:    Translation:Cells
    45. Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray-derived conformational ensembles. Proc Natl Acad Sci U S A. 2020 12 29; 117(52):33204-33215. Yabukarski F, Biel JT, Pinney MM, Doukov T, Powers AS, Fraser JS, Herschlag D. PMID: 33376217; PMCID: PMC7776779.
      View in: PubMed   Mentions: 26     Fields:    Translation:Cells
    46. Genetic interaction mapping informs integrative structure determination of protein complexes. Science. 2020 12 11; 370(6522). Braberg H, Echeverria I, Bohn S, Cimermancic P, Shiver A, Alexander R, Xu J, Shales M, Dronamraju R, Jiang S, Dwivedi G, Bogdanoff D, Chaung KK, Hüttenhain R, Wang S, Mavor D, Pellarin R, Schneidman D, Bader JS, Fraser JS, Morris J, Haber JE, Strahl BD, Gross CA, Dai J, Boeke JD, Sali A, Krogan NJ. PMID: 33303586; PMCID: PMC7946025.
      View in: PubMed   Mentions: 13     Fields:    Translation:AnimalsCells
    47. qFit 3: Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps. Protein Sci. 2021 01; 30(1):270-285. Riley BT, Wankowicz SA, de Oliveira SHP, van Zundert GCP, Hogan DW, Fraser JS, Keedy DA, van den Bedem H. PMID: 33210433; PMCID: PMC7737783.
      View in: PubMed   Mentions: 19     Fields:    
    48. Discovery of allosteric binding sites by crystallographic fragment screening. Curr Opin Struct Biol. 2020 12; 65:209-216. Krojer T, Fraser JS, von Delft F. PMID: 33171388; PMCID: PMC10979522.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    49. DNA-binding proteins meet their mismatch. Nature. 2020 11; 587(7833):199-200. Kundert K, Fraser JS. PMID: 33087865.
      View in: PubMed   Mentions: 2     Fields:    
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    97. 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. Dellus-Gur E, Elias M, Caselli E, Prati F, Salverda ML, de Visser JA, Fraser JS, Tawfik DS. PMID: 26004540; PMCID: PMC4718737.
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    98. 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. 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. PMID: 25981045; PMCID: PMC4613747.
      View in: PubMed   Mentions: 33     Fields:    Translation:HumansAnimalsCells
    99. Integrative, dynamic structural biology at atomic resolution--it's about time. Nat Methods. 2015 Apr; 12(4):307-18. van den Bedem H, Fraser JS. PMID: 25825836; PMCID: PMC4457290.
      View in: PubMed   Mentions: 101     Fields:    Translation:Cells
    100. Keep on moving: discovering and perturbing the conformational dynamics of enzymes. Acc Chem Res. 2015 Feb 17; 48(2):423-30. Bhabha G, Biel JT, Fraser JS. PMID: 25539415; PMCID: PMC4334266.
      View in: PubMed   Mentions: 37     Fields:    Translation:HumansCells
    101. 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. Wall ME, Van Benschoten AH, Sauter NK, Adams PD, Fraser JS, Terwilliger TC. PMID: 25453071; PMCID: PMC4273327.
      View in: PubMed   Mentions: 31     Fields:    Translation:Cells
    102. Discovery and characterization of gut microbiota decarboxylases that can produce the neurotransmitter tryptamine. Cell Host Microbe. 2014 Oct 08; 16(4):495-503. Williams BB, Van Benschoten AH, Cimermancic P, Donia MS, Zimmermann M, Taketani M, Ishihara A, Kashyap PC, Fraser JS, Fischbach MA. PMID: 25263219; PMCID: PMC4260654.
      View in: PubMed   Mentions: 271     Fields:    Translation:HumansCells
    103. E pluribus unum, no more: from one crystal, many conformations. Curr Opin Struct Biol. 2014 Oct; 28:56-62. Woldeyes RA, Sivak DA, Fraser JS. PMID: 25113271; PMCID: PMC4253534.
      View in: PubMed   Mentions: 29     Fields:    Translation:Cells
    104. Crystal cryocooling distorts conformational heterogeneity in a model Michaelis complex of DHFR. Structure. 2014 Jun 10; 22(6):899-910. Keedy DA, van den Bedem H, Sivak DA, Petsko GA, Ringe D, Wilson MA, Fraser JS. PMID: 24882744; PMCID: PMC4082491.
      View in: PubMed   Mentions: 81     Fields:    Translation:Cells
    105. Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery. Nat Chem. 2014 Jul; 6(7):575-83. Fischer M, Coleman RG, Fraser JS, Shoichet BK. PMID: 24950326; PMCID: PMC4144196.
      View in: PubMed   Mentions: 60     Fields:    Translation:Cells
    106. Diffuse X-ray scattering to model protein motions. Structure. 2014 Feb 04; 22(2):182-4. Wall ME, Adams PD, Fraser JS, Sauter NK. PMID: 24507780; PMCID: PMC4070675.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    107. 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. Fenwick RB, van den Bedem H, Fraser JS, Wright PE. PMID: 24474795; PMCID: PMC3910589.
      View in: PubMed   Mentions: 77     Fields:    Translation:Cells
    108. 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. Lang PT, Holton JM, Fraser JS, Alber T. PMID: 24363322; PMCID: PMC3890839.
      View in: PubMed   Mentions: 39     Fields:    Translation:HumansCells
    109. From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II. Cell. 2013 Aug 15; 154(4):775-88. 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. PMID: 23932120; PMCID: PMC3932829.
      View in: PubMed   Mentions: 89     Fields:    Translation:AnimalsCells
    110. Automated identification of functional dynamic contact networks from X-ray crystallography. Nat Methods. 2013 Sep; 10(9):896-902. van den Bedem H, Bhabha G, Yang K, Wright PE, Fraser JS. PMID: 23913260; PMCID: PMC3760795.
      View in: PubMed   Mentions: 76     Fields:    Translation:HumansCells
    111. From systems to structure: bridging networks and mechanism. Mol Cell. 2013 Jan 24; 49(2):222-31. Fraser JS, Gross JD, Krogan NJ. PMID: 23352243; PMCID: PMC3558917.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansAnimals
    112. Flexible backbone sampling methods to model and design protein alternative conformations. Methods Enzymol. 2013; 523:61-85. Ollikainen N, Smith CA, Fraser JS, Kortemme T. PMID: 23422426; PMCID: PMC3750959.
      View in: PubMed   Mentions: 22     Fields:    Translation:Cells
    113. CheShift-2 resolves a local inconsistency between two X-ray crystal structures. J Biomol NMR. 2012 Oct; 54(2):193-8. Vila JA, Sue SC, Fraser JS, Scheraga HA, Dyson HJ. PMID: 22945426; PMCID: PMC3471536.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    114. Systematic functional prioritization of protein posttranslational modifications. Cell. 2012 Jul 20; 150(2):413-25. Beltrao P, Albanèse V, Kenner LR, Swaney DL, Burlingame A, Villén J, Lim WA, Fraser JS, Frydman J, Krogan NJ. PMID: 22817900; PMCID: PMC3404735.
      View in: PubMed   Mentions: 207     Fields:    Translation:HumansAnimalsCells
    115. 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. Kapp GT, Liu S, Stein A, Wong DT, Reményi A, Yeh BJ, Fraser JS, Taunton J, Lim WA, Kortemme T. PMID: 22403064; PMCID: PMC3325720.
      View in: PubMed   Mentions: 39     Fields:    Translation:AnimalsCells
    116. Accessing protein conformational ensembles using room-temperature X-ray crystallography. Proc Natl Acad Sci U S A. 2011 Sep 27; 108(39):16247-52. Fraser JS, van den Bedem H, Samelson AJ, Lang PT, Holton JM, Echols N, Alber T. PMID: 21918110; PMCID: PMC3182744.
      View in: PubMed   Mentions: 292     Fields:    Translation:Cells
    117. Mining electron density for functionally relevant protein polysterism in crystal structures. Cell Mol Life Sci. 2011 Jun; 68(11):1829-41. Fraser JS, Jackson CJ. PMID: 21190057; PMCID: PMC3092063.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimalsCells
    118. The tumor-associated EpCAM regulates morphogenetic movements through intracellular signaling. J Cell Biol. 2010 Nov 01; 191(3):645-59. Maghzal N, Vogt E, Reintsch W, Fraser JS, Fagotto F. PMID: 20974811; PMCID: PMC3003323.
      View in: PubMed   Mentions: 43     Fields:    Translation:HumansAnimalsCells
    119. Automated electron-density sampling reveals widespread conformational polymorphism in proteins. Protein Sci. 2010 Jul; 19(7):1420-31. Lang PT, Ng HL, Fraser JS, Corn JE, Echols N, Sales M, Holton JM, Alber T. PMID: 20499387; PMCID: PMC2974833.
      View in: PubMed   Mentions: 92     Fields:    Translation:Cells
    120. Hidden alternative structures of proline isomerase essential for catalysis. Nature. 2009 Dec 03; 462(7273):669-73. Fraser JS, Clarkson MW, Degnan SC, Erion R, Kern D, Alber T. PMID: 19956261; PMCID: PMC2805857.
      View in: PubMed   Mentions: 252     Fields:    Translation:HumansCells
    121. Immunoglobulin-like domains on bacteriophage: weapons of modest damage? Curr Opin Microbiol. 2007 Aug; 10(4):382-7. Fraser JS, Maxwell KL, Davidson AR. PMID: 17765600.
      View in: PubMed   Mentions: 50     Fields:    Translation:Cells
    122. 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. Fraser JS, Merlie JP, Echols N, Weisfield SR, Mignot T, Wemmer DE, Zusman DR, Alber T. PMID: 17573816; PMCID: PMC1974792.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    123. Ig-like domains on bacteriophages: a tale of promiscuity and deceit. J Mol Biol. 2006 Jun 02; 359(2):496-507. Fraser JS, Yu Z, Maxwell KL, Davidson AR. PMID: 16631788.
      View in: PubMed   Mentions: 115     Fields:    Translation:AnimalsCells
    124. Improving treatment services for substance abusers with comorbid depression. Am J Addict. 2004 May-Jun; 13(3):295-304. Womack S, Compton WM, Dennis M, McCormick S, Fraser J, Horton JC, Spitznagel EL, Cottler LB. PMID: 15370949.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCTClinical Trials
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