Publications


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 Research. 2017.

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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. Journal of Synchrotron Radiation. 2017.

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Biel JT, Thompson MC, Cunningham CN, Corn JE, Fraser JS. Flexibility and design: conformational heterogeneity along the evolutionary trajectory of a redesigned ubiquitin. Submitted. 2016.

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Wang RYR, Song Y, Barad BA, Cheng Y, Fraser JS, DiMaio F. Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta. eLife. 2016.

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Mavor D, Barlow KA, Thompson S, Barad BA, Bonny AR, Cario CL, Gaskins G, Liu Z, Deming L, Axen SD, Caceres E, Chen W, Cuesta A, Gate R, 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 E, See S, 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.

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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. Proceedings of the National Academy of Sciences, 2016.

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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 AMJJ, Borek D, Brett TJ, Caflisch A, Chang C, Chazin WJ, Corbett KD, Cosgrove MS, Crosson S, Dhe-Paganon S, Cera ED, Drennan CL, Eck MJ, Eichman BF, Fan QR, Ferré-DAmaré 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 PJB, 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 FRNC, Gonen T, Kirchhausen T, Diederichs K, Crosas M, Sliz P. Data publication with the structural biology data grid supports live analysis. Nature Communications, 2016.

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Cimermancic P, Weinkam P, Rettenmaier TJ, Bichmann L, Keedy DA, Woldeyes RA, Schneidmann D, Demerdash ONA, Mitchell JC, Wells JA, Fraser JS, Sali A. CryptoSite: Expanding the druggable proteome by characterization and prediction of cryptic binding sites. Journal of Molecular Biology. 2016

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Baxter EL, Aguila L, Alonso-Mori R, Barnes CO, BonaguraCA, 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. Acta Crystallographica D. 2016

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Thomaston JL, Alfonso-Prieto M, Woldeyes RA, Fraser JS, Klein ML, Fiorin G, DeGrado WF. High resolution structures of the M2 proton channel from influenza A virus reveal dynamic pathways for proton stabilization and transduction. Proceedings of the National Academy of Sciences, 2015.

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Fischer M, Shoichet BK, Fraser JS. One Crystal, two Temperatures – Cryocooling Penalties alter Ligand Binding to Transient Protein Sites. ChemBioChem. 2015.

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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. Journal of Molecular Biology. 2015.

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Kane JR, Stanley DJ, Hultquist JF, Johnson JR, Mietrach N, Binning JM, Jonsson SR, Barelier S, Newton BW, Johnson TL, Franks-Skiba KE, Li M, Brown WL, Gunnarsson HI, Adalbjornsdottir A, Fraser JS, Harris RS, Andresdottir 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 Reports. 2015.

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Keedy DA, Fraser JS, van den Bedem H. Exposing hidden alternative backbone conformations in X-ray crystallography using qFit. PLOS Computational Biology. 2015.

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van den Bedem H, Fraser JS. Integrative, Dynamic Structural Biology at Atomic Resolution — It’s About Time. Nature Methods. 2015.

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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.

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Barad BA, Echols N, Wang RYR, Cheng Y, DiMaio F, Adams PD, Fraser JS. EMRinger: Side-chain-directed model and map validation for 3D Electron Cryomicroscopy. Nature Methods. 2015.

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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 Crystallographica D. 2015.

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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 Crystallographica D. 2015.

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Bhabha G, Biel JT, Fraser JS. Keep on Moving: Discovering and Perturbing the Conformational Dynamics of Enzymes. Accounts of Chemical Research. 2015.

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Wall ME, VanBenschoten 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. Proceedings of the National Academy of Sciences. 2014

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Williams BB, VanBenschoten AH, Cimermancic P, Donia MS, Zimmermann M, Taketani M, Ishihara A, Kashyap PC, Fraser JS, Fischbach MA. Discovery and characterization of two tryptamine-producing decarboxylases from the gut microbiota. Cell Host and Microbe. 2014.

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Woldeyes RA, Sivak DA, Fraser JS. E pluribus unum, no more: from one crystal, many conformations. Current Opinion in Structural Biology. 2014.

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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.

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Fischer M*, Coleman RG*, Fraser JS, Shoichet BK. Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery. Nature Chemistry. 2014.

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Wall ME, Adams PD, Fraser JS, Sauter NK. Diffuse X-ray Scattering to Model Protein Motions. Structure. 2014

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Fenwick RB, van den Bedem H, Fraser JS, Wright PE. Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR. Proceedings of the National Academy of Sciences. 2014.

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Lang PT, Holton JM, Fraser JS, Alber T. Protein structural ensembles are revealed by redefining X-ray electron density noise. Proceedings of the National Academy of Sciences. 2014.

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van den Bedem H, Bhabha G, Yang K, Wright PE, Fraser JS. Automated identification of functional dynamic contact networks from X-ray crystallography. Nature Methods. 2013.

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Braberg H, Jin H, Moehle E, Chan YA, Wang S, Shales M, Benschop JJ, Morris JH, Fraser JS, Qiu C, Hu F, Tang LK, Holstege FCP, Hieter P, Guthrie C, Kaplan CD, Krogan NJ. From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II. Cell. 2013.

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Ollikainen N, Smith CA, Fraser JS, Kortemme T. Flexible Backbone Sampling Methods to Model and Design Protein Alternative Conformations. Methods in Enzymology. 2013.

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Fraser JS, Gross JD, Krogan NJ. From Systems to Structure: Bridging Networks and Mechanism. Molecular Cell. 2013.

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Vila JA, Sue SC, Fraser JS, Scheraga HA, Dyson HJ. CheShift-2 resolves a local inconsistency between two X-ray crystal structures. Journal of Biomolecular NMR. 2012.

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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.

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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. Proceedings of the National Academy of Sciences. 2012.

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Fraser JS, van den Bedem H, Samelson AJ, Lang PT, Holton JM, Echols N, Alber T. Accessing protein conformational ensembles by room-temperature X-ray crystallography. Proceedings of the National Academy of Sciences. 2011.

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Fraser JS, Jackson CJ. Mining electron density for functionally relevant protein polysterism in crystal structures. Cellular and Molecular Life Sciences. 2011.

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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 Science. 2010.

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Maghzal N*, Vogt E*, Reintsch W, Fraser JS, Fagotto F. The tumor-associated EpCAM regulates morphogenetic movements through intracellular signaling. Journal of Cell Biology. 2010.

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Fraser JS, Clarkson MW, Degnan SC, Erion R, Kern D, Alber T. Hidden alternative structures of proline isomerase essential for catalysis. Nature. 2009.

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Fraser JS, Maxwell KL, Davidson, AR. Immunoglobulin-Like Domains on Bacteriophage: Weapons of Modest Damage? Current Opinion in Microbiology. 2007.

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Fraser JS*, Merlie Jr. JP*, Echols N*, Weisfield SR, Mignot T, Wemmer DE, Zusman D, Alber T. An atypical receiver domain controls the dynamic polar localization of the Myxococcus xanthus social motility protein FrzS. Molecular Microbiology. 2007.

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Fraser JS, Yu Z, Maxwell KL, Davidson AR. Ig-like domains on bacteriophages: a tale of promiscuity and deceit. Journal of Molecular Biology. 2006.

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