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James Fraser, PhD

Title(s)Associate Professor, Bioengineering
SchoolSchool of Pharmacy
Address600 16th St
San Francisco CA 94158
Phone415-493-8421
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

    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/NIGMS R01GM123159Jan 1, 2018 - Dec 31, 2021
    Role: Principal Investigator
    Model Comparison in Structural Biology
    NIH/NIGMS R21GM110580Apr 1, 2014 - Mar 31, 2016
    Role: Principal Investigator
    The Impact of Mutation on the Conformations and Recognition of Ubiquitin
    NIH DP5OD009180Sep 20, 2011 - Aug 31, 2016
    Role: Principal Investigator

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    Collapse In The News
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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. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020 Apr 30. Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Huettenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Meyer B, Roesch F, Vallet T, Mac Kain A, Miorin L, Moreno E, Naing ZZC, Zhou Y, Peng S, Shi Y, Zhang Z, Shen W, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Lyu J, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Rakesh R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Huang XP, Liu Y, Wankowicz SA, Bohn M, Safari M, Ugur FS, Koh C, Savar NS, Tran QD, Shengjuler D, Fletcher SJ, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, Sharp PP, Wenzell NA, Kuzuoglu D, Wang HY, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Stroud RM, Frankel AD, Rosenberg OS, Verba KA, Agard DA, Ott M, Emerman M, Jura N, von Zastrow M, Verdin E, Ashworth A, Schwartz O, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor SN, Fraser JS, Gross JD, Sali A, Roth BL, Ruggero D, Taunton J, Kortemme T, Beltrao P, Vignuzzi M, García-Sastre A, Shokat KM, Shoichet BK, Krogan NJ. PMID: 32353859.
      View in: PubMed   Mentions: 55     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    2. A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing. bioRxiv. 2020 Mar 22. Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O'Meara MJ, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Naing ZZC, Zhou Y, Peng S, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Shen W, Shi Y, Zhang Z, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Ramachandran R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Lin Y, Wankowicz SA, Bohn M, Trenker R, Young JM, Cavero D, Hiatt J, Roth T, Rathore U, Subramanian A, Noack J, Hubert M, Roesch F, Vallet T, Meyer B, White KM, Miorin L, Agard D, Emerman M, Ruggero D, García-Sastre A, Jura N, von Zastrow M, Taunton J, Schwartz O, Vignuzzi M, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor S, Fraser JS, Gross J, Sali A, Kortemme T, Beltrao P, Shokat K, Shoichet BK, Krogan NJ. PMID: 32511329.
      View in: PubMed   Mentions:
    3. Assessment of the nucleotide modifications in the high-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit. Nucleic Acids Res. 2020 03 18; 48(5):2723-2732. Stojkovic V, Myasnikov AG, Young ID, Frost A, Fraser JS, Fujimori DG. PMID: 31989172.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    4. Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals. IUCrJ. 2020 Mar 01; 7(Pt 2):306-323. Wolff AM, Young ID, Sierra RG, Brewster AS, Martynowycz MW, Nango E, Sugahara M, Nakane T, Ito K, Aquila A, Bhowmick A, Biel JT, Carbajo S, Cohen AE, Cortez S, Gonzalez A, Hino T, Im D, Koralek JD, Kubo M, Lazarou TS, Nomura T, Owada S, Samelson AJ, Tanaka T, Tanaka R, Thompson EM, van den Bedem H, Woldeyes RA, Yumoto F, Zhao W, Tono K, Boutet S, Iwata S, Gonen T, Sauter NK, Fraser JS, Thompson MC. PMID: 32148858.
      View in: PubMed   Mentions:
    5. What Will Computational Modeling Approaches Have to Say in the Era of Atomistic Cryo-EM Data? J Chem Inf Model. 2020 May 26; 60(5):2410-2412. Fraser JS, Lindorff-Larsen K, Bonomi M. PMID: 32090567.
      View in: PubMed   Mentions:    Fields:    
    6. Differences in the chitinolytic activity of mammalian chitinases on soluble and insoluble substrates. Protein Sci. 2020 04; 29(4):966-977. Barad BA, Liu L, Diaz RE, Basilio R, Van Dyken SJ, Locksley RM, Fraser JS. PMID: 31930591.
      View in: PubMed   Mentions:    Fields:    
    7. Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein. Struct Dyn. 2019 Nov; 6(6):064704. Wych DC, Fraser JS, Mobley DL, Wall ME. PMID: 31867408.
      View in: PubMed   Mentions:
    8. Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis. Proc Natl Acad Sci U S A. 2019 12 17; 116(51):25634-25640. Dasgupta M, Budday D, de Oliveira SHP, Madzelan P, Marchany-Rivera D, Seravalli J, Hayes B, Sierra RG, Boutet S, Hunter MS, Alonso-Mori R, Batyuk A, Wierman J, Lyubimov A, Brewster AS, Sauter NK, Applegate GA, Tiwari VK, Berkowitz DB, Thompson MC, Cohen AE, Fraser JS, Wall ME, van den Bedem H, Wilson MA. PMID: 31801874.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    9. Computational design of a modular protein sense-response system. Science. 2019 11 22; 366(6468):1024-1028. Glasgow AA, Huang YM, Mandell DJ, Thompson M, Ritterson R, Loshbaugh AL, Pellegrino J, Krivacic C, Pache RA, Barlow KA, Ollikainen N, Jeon D, Kelly MJS, Fraser JS, Kortemme T. PMID: 31754004.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    10. Co-occurring Alterations in the RAS-MAPK Pathway Limit Response to MET Inhibitor Treatment in MET Exon 14 Skipping Mutation-Positive Lung Cancer. Clin Cancer Res. 2020 Jan 15; 26(2):439-449. Rotow JK, Gui P, Wu W, Raymond VM, Lanman RB, Kaye FJ, Peled N, Fece de la Cruz F, Nadres B, Corcoran RB, Yeh I, Bastian BC, Starostik P, Newsom K, Olivas VR, Wolff AM, Fraser JS, Collisson EA, McCoach CE, Camidge DR, Pacheco J, Bazhenova L, Li T, Bivona TG, Blakely CM. PMID: 31548343.
      View in: PubMed   Mentions:    Fields:    
    11. Temperature-jump solution X-ray scattering reveals distinct motions in a dynamic enzyme. Nat Chem. 2019 11; 11(11):1058-1066. Thompson MC, Barad BA, Wolff AM, Sun Cho H, Schotte F, Schwarz DMC, Anfinrud P, Fraser JS. PMID: 31527847.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    12. Synthetic Essentiality of Metabolic Regulator PDHK1 in PTEN-Deficient Cells and Cancers. Cell Rep. 2019 08 27; 28(9):2317-2330.e8. Chatterjee N, Pazarentzos E, Mayekar MK, Gui P, Allegakoen DV, Hrustanovic G, Olivas V, Lin L, Verschueren E, Johnson JR, Hofree M, Yan JJ, Newton BW, Dollen JV, Earnshaw CH, Flanagan J, Chan E, Asthana S, Ideker T, Wu W, Suzuki J, Barad BA, Kirichok Y, Fraser JS, Weiss WA, Krogan NJ, Tulpule A, Sabnis AJ, Bivona TG. PMID: 31461649.
      View in: PubMed   Mentions:    Fields:    
    13. Biomaterials in non-integer dimensions. Nat Chem. 2019 07; 11(7):599-600. Young ID, Fraser JS. PMID: 31209301.
      View in: PubMed   Mentions:    Fields:    
    14. Effects of a-tubulin acetylation on microtubule structure and stability. Proc Natl Acad Sci U S A. 2019 05 21; 116(21):10366-10371. Eshun-Wilson L, Zhang R, Portran D, Nachury MV, Toso DB, Löhr T, Vendruscolo M, Bonomi M, Fraser JS, Nogales E. PMID: 31072936.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    15. Biophysical Characterization of a Disabled Double Mutant of Soybean Lipoxygenase: The "Undoing" of Precise Substrate Positioning Relative to Metal Cofactor and an Identified Dynamical Network. J Am Chem Soc. 2019 01 30; 141(4):1555-1567. Hu S, Offenbacher AR, Thompson EM, Gee CL, Wilcoxen J, Carr CAM, Prigozhin DM, Yang V, Alber T, Britt RD, Fraser JS, Klinman JP. PMID: 30645119.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    16. qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps. J Med Chem. 2018 12 27; 61(24):11183-11198. van Zundert GCP, Hudson BM, de Oliveira SHP, Keedy DA, Fonseca R, Heliou A, Suresh P, Borrelli K, Day T, Fraser JS, van den Bedem H. PMID: 30457858.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    17. A Multi-model Approach to Assessing Local and Global Cryo-EM Map Quality. Structure. 2019 02 05; 27(2):344-358.e3. Herzik MA, Fraser JS, Lander GC. PMID: 30449687.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    18. Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance. Biol Open. 2018 Jul 23; 7(7). Mavor D, Barlow KA, Asarnow D, Birman Y, Britain D, Chen W, Green EM, Kenner LR, Mensa B, Morinishi LS, Nelson CA, Poss EM, Suresh P, Tian R, Arhar T, Ary BE, Bauer DP, Bergman ID, Brunetti RM, Chio CM, Dai SA, Dickinson MS, Elledge SK, Helsell CVM, Hendel NL, Kang E, Kern N, Khoroshkin MS, Kirkemo LL, Lewis GR, Lou K, Marin WM, Maxwell AM, McTigue PF, Myers-Turnbull D, Nagy TL, Natale AM, Oltion K, Pourmal S, Reder GK, Rettko NJ, Rohweder PJ, Schwarz DMC, Tan SK, Thomas PV, Tibble RW, Town JP, Tsai MK, Ugur FS, Wassarman DR, Wolff AM, Wu TS, Bogdanoff D, Li J, Thorn KS, O'Conchúir S, Swaney DL, Chow ED, Madhani HD, Redding S, Bolon DN, Kortemme T, DeRisi JL, Kampmann M, Fraser JS. PMID: 30037883.
      View in: PubMed   Mentions:
    19. An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering. Elife. 2018 06 07; 7. Keedy DA, Hill ZB, Biel JT, Kang E, Rettenmaier TJ, Brandão-Neto J, Pearce NM, von Delft F, Wells JA, Fraser JS. PMID: 29877794.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    20. Rescue of conformational dynamics in enzyme catalysis by directed evolution. Nat Commun. 2018 04 03; 9(1):1314. Otten R, Liu L, Kenner LR, Clarkson MW, Mavor D, Tawfik DS, Kern D, Fraser JS. PMID: 29615624.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    21. Bringing diffuse X-ray scattering into focus. Curr Opin Struct Biol. 2018 06; 50:109-116. Wall ME, Wolff AM, Fraser JS. PMID: 29455056.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    22. 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. 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. PMID: 28835537.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    23. 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. Acker TM, Gable JE, Bohn MF, Jaishankar P, Thompson MC, Fraser JS, Renslo AR, Craik CS. PMID: 28759216.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    24. 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. Offenbacher AR, Hu S, Poss EM, Carr CAM, Scouras AD, Prigozhin DM, Iavarone AT, Palla A, Alber T, Fraser JS, Klinman JP. PMID: 28691068.
      View in: PubMed   Mentions:
    25. Flexibility and Design: Conformational Heterogeneity along the Evolutionary Trajectory of a Redesigned Ubiquitin. Structure. 2017 05 02; 25(5):739-749.e3. Biel JT, Thompson MC, Cunningham CN, Corn JE, Fraser JS. PMID: 28416112.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    26. Cytidine deaminase efficiency of the lentiviral viral restriction factor APOBEC3C correlates with dimerization. Nucleic Acids Res. 2017 04 07; 45(6):3378-3394. Adolph MB, Ara A, Feng Y, Wittkopp CJ, Emerman M, Fraser JS, Chelico L. PMID: 28158858.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    27. Conformational variation of proteins at room temperature is not dominated by radiation damage. J Synchrotron Radiat. 2017 01 01; 24(Pt 1):73-82. Russi S, González A, Kenner LR, Keedy DA, Fraser JS, van den Bedem H. PMID: 28009548.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    28. Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta. Elife. 2016 09 26; 5. Wang RY, Song Y, Barad BA, Cheng Y, Fraser JS, DiMaio F. PMID: 27669148.
      View in: PubMed   Mentions: 47     Fields:    
    29. SCIENTIFIC COMMUNITY. Preprints for the life sciences. Science. 2016 May 20; 352(6288):899-901. 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. PMID: 27199406.
      View in: PubMed   Mentions: 21     Fields:    
    30. Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting. Elife. 2016 04 25; 5. 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. PMID: 27111525.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimals
    31. Measuring and modeling diffuse scattering in protein X-ray crystallography. Proc Natl Acad Sci U S A. 2016 Apr 12; 113(15):4069-74. Van Benschoten AH, Liu L, Gonzalez A, Brewster AS, Sauter NK, Fraser JS, Wall ME. PMID: 27035972.
      View in: PubMed   Mentions: 10     Fields:    
    32. Data publication with the structural biology data grid supports live analysis. Nat Commun. 2016 Mar 07; 7:10882. 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. PMID: 26947396.
      View in: PubMed   Mentions: 34     Fields:    
    33. CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites. J Mol Biol. 2016 Feb 22; 428(4):709-719. 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. PMID: 26854760.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    34. High-density grids for efficient data collection from multiple crystals. Acta Crystallogr D Struct Biol. 2016 Jan; 72(Pt 1):2-11. 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. PMID: 26894529.
      View in: PubMed   Mentions:
    35. 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. Thomaston JL, Alfonso-Prieto M, Woldeyes RA, Fraser JS, Klein ML, Fiorin G, DeGrado WF. PMID: 26578770.
      View in: PubMed   Mentions: 23     Fields:    Translation:Cells
    36. Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit. PLoS Comput Biol. 2015 Oct; 11(10):e1004507. Keedy DA, Fraser JS, van den Bedem H. PMID: 26506617.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    37. Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography. Elife. 2015 Sep 30; 4. 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. PMID: 26422513.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansCells
    38. EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy. Nat Methods. 2015 Oct; 12(10):943-6. Barad BA, Echols N, Wang RY, Cheng Y, DiMaio F, Adams PD, Fraser JS. PMID: 26280328.
      View in: PubMed   Mentions: 115     Fields:    Translation:Cells
    39. 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. Urzhumtsev A, Afonine PV, Van Benschoten AH, Fraser JS, Adams PD. PMID: 26249348.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    40. Predicting X-ray diffuse scattering from translation-libration-screw structural ensembles. Acta Crystallogr D Biol Crystallogr. 2015 Aug; 71(Pt 8):1657-67. Van Benschoten AH, Afonine PV, Terwilliger TC, Wall ME, Jackson CJ, Sauter NK, Adams PD, Urzhumtsev A, Fraser JS. PMID: 26249347.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    41. One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites. Chembiochem. 2015 Jul 27; 16(11):1560-4. Fischer M, Shoichet BK, Fraser JS. PMID: 26032594.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    42. Negative Epistasis and Evolvability in TEM-1 ß-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.
      View in: PubMed   Mentions: 23     Fields:    Translation:Cells
    43. 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.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansAnimalsCells
    44. 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.
      View in: PubMed   Mentions: 57     Fields:    Translation:Cells
    45. 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.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansCells
    46. 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.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    47. 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.
      View in: PubMed   Mentions: 56     Fields:    Translation:HumansCells
    48. 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.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    49. 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.
      View in: PubMed   Mentions: 35     Fields:    Translation:Cells
    50. 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.
      View in: PubMed   Mentions: 30     Fields:    Translation:Cells
    51. 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.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    52. 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.
      View in: PubMed   Mentions: 43     Fields:    Translation:Cells
    53. 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.
      View in: PubMed   Mentions: 30     Fields:    Translation:HumansCells
    54. 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.
      View in: PubMed   Mentions: 56     Fields:    Translation:AnimalsCells
    55. 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.
      View in: PubMed   Mentions: 49     Fields:    Translation:HumansCells
    56. 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.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimals
    57. 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.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    58. 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.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    59. 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.
      View in: PubMed   Mentions: 137     Fields:    Translation:HumansAnimalsCells
    60. 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.
      View in: PubMed   Mentions: 29     Fields:    Translation:AnimalsCells
    61. 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.
      View in: PubMed   Mentions: 161     Fields:    Translation:Cells
    62. 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.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    63. 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.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansAnimalsCells
    64. 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.
      View in: PubMed   Mentions: 62     Fields:    Translation:Cells
    65. 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.
      View in: PubMed   Mentions: 177     Fields:    Translation:HumansCells
    66. 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: 32     Fields:    Translation:Cells
    67. 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.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    68. 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: 65     Fields:    Translation:AnimalsCells
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