Publications


A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing.

Gordon DE*, Jang GM*, Bouhaddou M*, Xu J*, Obernier K*, White KM*, O’Meara MJ*, Rezelj VV*, Guo JZ, Swaney DL, Tummino TA, Huttenhain 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 D, 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 S, 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. Nature. 2020.



Expanding the space of protein geometries by computational design of ​de novo fold families.

Pan X, Thompson M, Zhang Y, Liu L, Fraser JS, Kelly MJS, Kortemme T. Submitted - Preprint on Biorxiv. 2020.

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Evolution of an enzyme conformational ensemble guides design of an efficient biocatalyst.

Broom A*, Rakotoharisoa RV*, Thompson MC, Zarifi N, Nguyen E, Mukhametzhanov N, Liu L, Fraser JS, Chica RA. Submitted - Preprint on BioRxiv. 2020.

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Assessment of the nucleotide modifications in the high-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit.

Stojković V, Myasnikov AG, Young ID, Frost A, Fraser JS, Fujimori DG. Nucleic Acids Research. 2020.

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Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals.

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 A, Tanaka R, Tanaka T, 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. IUCrJ. 2020.



What will computational modelling approaches have to say in the era of atomistic cryo-EM data?

Fraser JS, Lindorff-Larsen K, Bonomi M. Journal of Chemical Information and Modeling. 2020.



Co-occurring alterations in the RAS-MAPK pathway limit response to MET inhibitor treatment in MET exon 14 skipping mutation-positive lung cancer.

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 V, Wolff AM, Fraser JS, Collisson EA, McCoach CE, Camidge DR, Pacheco J, Bazhenova L, Li T, Bivona TG, Blakely CM. Clinical Cancer Research. 2020.

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Differences in the chitinolytic activity of mammalian chitinases on soluble and insoluble substrates.

Barad BA, Liu L, Diaz RE, Basillo R, Van Dyken SJ, Locksley RM, Fraser JS. Protein Science. 2020.



Ensemble refinement produces consistent R-free values but smaller ensemble sizes than previously reported.

Wankowicz SA, Fraser JS. Computational Crystallography Newsletter. 2020.



Liquid-like and rigid-body motions in molecular dynamics simulations of a crystalline protein.

Wych DC, Fraser JS, Mobley DL, Wall ME. Structural Dynamics. 2019.



Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis.

Dasgupta M, Budday D, 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. PNAS. 2019.



Computational design of a modular protein sense/response system.

Glasgow AA*, Huang Y*, 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. Science. 2019.



Assessing positioning in enzymatic catalysis via ketosteroid isomerase conformational ensembles.

Yabukarski F, Biel JT, Pinney MM, Doukov T, Powers AS, Fraser JS, Herschlag D. Submitted - Preprint on BioRxiv. 2019.

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Temperature-Jump Solution X-ray Scattering Reveals Distinct Motions in a Dynamic Enzyme.

Thompson MC, Barad BA, Wolff AM, Cho HS, Schotte F, Schwarz DMC, Anfinrud P, Fraser JS. Nature Chemistry. 2019.



Synthetic essentiality of metabolic regulator PDHK1 in PTEN-deficient cells and cancers.

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. Cell Reports. 2019.

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Synthesis and Mechanism of Action of Group a Streptogramin Antibiotics That Overcome Resistance.

Li Q*, Pellegrino J*, Lee DJ, Tran AA, Wang R, Park JE, Ji K, Chow D, Zhang N, Brilot AF, Biel JT, van Zundert G, Borrelli K, Shinabarger D, Wolfe C, Murray B, Jacobson MP, Fraser JS, Seiple IB. Submitted - Preprint on ChemRxiv. 2019.



News & Views: Biomaterials in non-integer dimensions.

Young ID, Fraser JS. Nature Chemistry. 2019.



Effects of α-tubulin acetylation on microtubule structure and stability.

Eshun-Wilson L, Zhang R, Portran D, Toso D, Lohr T, Vendruscolo M, Bonomi M, Fraser JS, Nogales E. PNAS. 2019.



A multi-model approach to assessing local and global cryo-EM map quality.

Herzik Jr. MA, Fraser JS, Lander GC. Structure. 2019.

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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.

Hu S, Offenbacher AR, Thompson EM, Gee CL, Wilcoxen J, Carr CAM, Prigozhin DM, Yang V, Alber T, Britt RD, Fraser JS, Klinman JP. JACS. 2019.

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qFit-ligand reveals widespread conformational heterogeneity of drug-like molecules in X-ray electron density maps.

van Zundert GCP*, Hudson BM*, Oliveira SHP, Keedy DA, Fonseca R, Heliou A, Suresh P, Borrelli K, Day T, Fraser JS, van den Bedem H. J Med Chem. 2018.



Model selection for biological crystallography.

Babcock NS, Keedy DA, Fraser JS, Sivak DA. Preprint on BioRxiv. 2018.



Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance.

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 CV M, 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. Biology Open. 2018.



An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering.

Keedy DA*, Hill ZB*, Biel JT, Kang E, Rettenmaier TJ, Brandao-Neto J, Pearce NM, von Delft F, Wells JA, Fraser JS. eLife. 2018.



Bringing Diffuse X-ray Scattering Into Focus.

Wall ME, Wolff AM, Fraser JS. Current Opinion in Structural Biology. 2018.



Rescue of Conformational Dynamics in Enzyme Catalysis by Directed Evolution.

Otten R*, Liu L*, Kenner LR, Clarkson MW, Mavor D, Tawfik DS, Kern D, Fraser JS. Nature Communications. 2018.

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XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction.

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. PNAS. 2017.

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Allosteric Inhibitors, Crystallography and Comparative Analysis Reveal Network of Coordinated Movement Across Human Herpesvirus Proteases.

Acker TM, Gable JE, Bohn MF, Jaishankar P, Thompson MC, Fraser JS, Renslo AR, Craik CS. JACS. 2017.

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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.

Offenbacher AR , Hu S, Poss EM, Carr CAM , Scouras AD, Prigozhin DM, Iavarone AT, Palla A, Alber T, Fraser JS, Klinman JP. ACS Central Science. 2017.

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Flexibility and design: conformational heterogeneity along the evolutionary trajectory of a redesigned ubiquitin.

Biel JT, Thompson MC, Cunningham CN, Corn JE, Fraser JS. Structure. 2017.



Cytidine deaminase efficiency of the lentiviral viral restriction factor APOBEC3C correlates with dimerization.

Adolph MB, Ara A, Feng Y, Wittkopp CJ, Emerman M, Fraser JS, Chelico L. Nucleic Acids Research. 2017.



Conformational variation of proteins at room temperature is not dominated by radiation damage.

Russi S, González A, Kenner LR, Keedy DA, Fraser JS, van den Bedem H. Journal of Synchrotron Radiation. 2017.

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Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta.

Wang RYR, Song Y, Barad BA, Cheng Y, Fraser JS, DiMaio F. eLife. 2016.

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Determination of Ubiquitin Fitness Landscapes Under Different Chemical Stresses in a Classroom Setting.

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. eLife. 2016.



Measuring and modeling diffuse scattering in protein X-ray crystallography.

Van Benschoten AH, Liu L, Gonzalez A, Brewster AS, Sauter NK, Fraser JS, Wall ME. PNAS, 2016.

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Data publication with the structural biology data grid supports live analysis.

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-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 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. Nature Communications, 2016.

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CryptoSite: Expanding the druggable proteome by characterization and prediction of cryptic binding sites.

Cimermancic P, Weinkam P, Rettenmaier TJ, Bichmann L, Keedy DA, Woldeyes RA, Schneidmann D, Demerdash ONA, Mitchell JC, Wells JA, Fraser JS, Sali A. Journal of Molecular Biology. 2016.



High-density grids for efficient data collection from multiple crystals.

Baxter EL, Aguila L, Alonso-Mori R, Barnes CO, BonaguraCA, Brehmer W, Brunger AT, Calero G, Caradoc-Davies TT, `jee 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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High resolution structures of the M2 proton channel from influenza A virus reveal dynamic pathways for proton stabilization and transduction.

Thomaston JL, Alfonso-Prieto M, Woldeyes RA, Fraser JS, Klein ML, Fiorin G, DeGrado WF. PNAS, 2015.

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Exposing hidden alternative backbone conformations in X-ray crystallography using qFit.

Keedy DA, Fraser JS, van den Bedem H. PLOS Computational Biology. 2015.



Mapping the Conformational Landscape of a Dynamic Enzyme by Multitemperature and XFEL Crystallography.

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. eLife. 2015.



EMRinger: Side-chain-directed model and map validation for 3D Electron Cryomicroscopy.

Barad BA, Echols N, Wang RYR, Cheng Y, DiMaio F, Adams PD, Fraser JS. Nature Methods. 2015.

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Predicting X-ray Diffuse Scattering from Translation Libration Screw Structural Ensembles.

Van Benschoten AH, Afonine PV, Terwilliger TC, Wall ME, Jackson CJ, Sauter NK, Adams PD, Urzhumtsev A, Fraser JS. Acta Crystallographica D. 2015.

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From deep TLS validation to ensembles of atomic models built from elemental motions.

Urzhumtsev A, Afonine PV, Van Benschoten AH, Fraser JS, Adams PD. Acta Crystallographica D. 2015.

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One Crystal, two Temperatures – Cryocooling Penalties alter Ligand Binding to Transient Protein Sites.

Fischer M, Shoichet BK, Fraser JS. ChemBioChem. 2015.



Negative epistasis and evolvability in TEM-1 β-lactamase – The thin line between an enzyme’s conformational freedom and disorder.

Dellus-Gur E, Elias M, Caselli E, Prati F, Salverda ML, de Visser JA, Fraser JS, Tawfik DS. Journal of Molecular Biology. 2015.

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Lineage-Specific Viral Hijacking of Non-canonical E3 Ubiquitin Ligase Cofactors in the Evolution of Vif Anti-APOBEC3 Activity.

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. Cell Reports. 2015.



Integrative, Dynamic Structural Biology at Atomic Resolution — It’s About Time.

van den Bedem H, Fraser JS. Nature Methods. 2015.

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Keep on Moving: Discovering and Perturbing the Conformational Dynamics of Enzymes.

Bhabha G, Biel JT, Fraser JS. Accounts of Chemical Research. 2015.

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Conformational Dynamics of a Crystalline Protein from Microsecond-Scale Molecular Dynamics Simulations and Diffuse X-Ray Scattering.

Wall ME, VanBenschoten AH, Sauter NK, Adams PD, Fraser JS, Terwilliger TC. PNAS. 2014.

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Discovery and characterization of two tryptamine-producing decarboxylases from the gut microbiota.

Williams BB, VanBenschoten AH, Cimermancic P, Donia MS, Zimmermann M, Taketani M, Ishihara A, Kashyap PC, Fraser JS, Fischbach MA. Cell Host and Microbe. 2014.



E pluribus unum, no more: from one crystal, many conformations.

Woldeyes RA, Sivak DA, Fraser JS. Current Opinion in Structural Biology. 2014.



Crystal Cryocooling Distorts Conformational Heterogeneity in a Model Michaelis Complex of DHFR.

Keedy DA, van den Bedem H, Sivak DA, Petsko GA, Ringe D, Wilson MA, Fraser JS. Structure. 2014.



Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery.

Fischer M*, Coleman RG*, Fraser JS, Shoichet BK. Nature Chemistry. 2014.



Diffuse X-ray Scattering to Model Protein Motions.

Wall ME, Adams PD, Fraser JS, Sauter NK. Structure. 2014.

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Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR.

Fenwick RB, van den Bedem H, Fraser JS, Wright PE. PNAS. 2014.

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Protein structural ensembles are revealed by redefining X-ray electron density noise.

Lang PT, Holton JM, Fraser JS, Alber T. PNAS. 2014.

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From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II.

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. Cell. 2013.



Automated identification of functional dynamic contact networks from X-ray crystallography.

van den Bedem H, Bhabha G, Yang K, Wright PE, Fraser JS. Nature Methods. 2013.



Flexible Backbone Sampling Methods to Model and Design Protein Alternative Conformations.

Ollikainen N, Smith CA, Fraser JS, Kortemme T. Methods in Enzymology. 2013.



From Systems to Structure: Bridging Networks and Mechanism.

Fraser JS, Gross JD, Krogan NJ. Molecular Cell. 2013.



CheShift-2 resolves a local inconsistency between two X-ray crystal structures.

Vila JA, Sue SC, Fraser JS, Scheraga HA, Dyson HJ. Journal of Biomolecular NMR. 2012.



Systematic functional prioritization of protein posttranslational modifications.

Beltrao P, Albanèse V, Kenner LR, Swaney DL, Burlingame A, Villén J, Lim WA, Fraser JS, Frydman J, Krogan NJ. Cell. 2012.



Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair.

Kapp GT*, Liu S*, Stein A, Wong DT, Reményi A, Yeh BJ, Fraser JS, Taunton J, Lim WA, Kortemme T. PNAS. 2012.



Accessing protein conformational ensembles by room-temperature X-ray crystallography.

Fraser JS, van den Bedem H, Samelson AJ, Lang PT, Holton JM, Echols N, Alber T. PNAS. 2011.



Mining electron density for functionally relevant protein polysterism in crystal structures.

Fraser JS, Jackson CJ. Cellular and Molecular Life Sciences. 2011.

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The tumor-associated EpCAM regulates morphogenetic movements through intracellular signaling.

Maghzal N*, Vogt E*, Reintsch W, Fraser JS, Fagotto F. Journal of Cell Biology. 2010.

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Automated electron-density sampling reveals widespread conformational polymorphism in proteins.

Lang PT*, Ng HL*, Fraser JS, Corn JE, Echols N, Sales M, Holton JM, Alber T. Protein Science. 2010.



Hidden alternative structures of proline isomerase essential for catalysis.

Fraser JS, Clarkson MW, Degnan SC, Erion R, Kern D, Alber T. Nature. 2009.



Immunoglobulin-Like Domains on Bacteriophage: Weapons of Modest Damage?

Fraser JS, Maxwell KL, Davidson, AR. Current Opinion in Microbiology. 2007.

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An atypical receiver domain controls the dynamic polar localization of the Myxococcus xanthus social motility protein FrzS.

Fraser JS*, Merlie Jr. JP*, Echols N*, Weisfield SR, Mignot T, Wemmer DE, Zusman D, Alber T. Molecular Microbiology. 2007.

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Ig-like domains on bacteriophages: a tale of promiscuity and deceit.

Fraser JS, Yu Z, Maxwell KL, Davidson AR. Journal of Molecular Biology. 2006.

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