James Fraser, PhD
Professor
Bioengineering
School of Pharmacy

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.

• Product-stabilized filamentation by human glutamine synthetase allosterically tunes activity.
  Biophysical Journal 2024 Eric R. Greene, Richard Muniz, Hiroki Yamamura, Samuel Hoff, Angelika Arada, Priyanka Bajaj, Daphne Chen, John D. Lee, Massimiliano Bonomi, Justin M. Kollman, James Fraser
• Role of conformational dynamics in the catalytic mechanism of viral macrodomains.
  Biophysical Journal 2024 Rishav Mitra, James Fraser
• Structure is beauty, but not always truth.
  Cell 2024 Fraser JS, Murcko MA
• MET variants with activating N-lobe mutations identified in hereditary papillary renal cell carcinomas still require ligand stimulation.
  bioRxiv : the preprint server for biology 2023 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
• Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography.
  Nature chemistry 2023 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,…
• A type 2 immune circuit in the stomach controls mammalian adaptation to dietary chitin.
  Science (New York, N.Y.) 2023 Kim DH, Wang Y, Jung H, Field RL, Zhang X, Liu TC, Ma C, Fraser JS, Brestoff JR, Van Dyken SJ
• A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication in vivo.
  PLoS pathogens 2023 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,…
• Chemoenzymatic Syntheses of Fluorine-18-Labeled Disaccharides from [18F] FDG Yield Potent Sensors of Living Bacteria In Vivo.
  Journal of the American Chemical Society 2023 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, …
• Conserved regulatory motifs in the juxtamembrane domain and kinase N-lobe revealed through deep mutational scanning of the MET receptor tyrosine kinase domain.
  bioRxiv : the preprint server for biology 2023 Estevam GO, Linossi EM, Macdonald CB, Espinoza CA, Michaud JM, Coyote-Maestas W, Collisson EA, Jura N, Fraser JS
• Refinement of multiconformer ensemble models from multi-temperature X-ray diffraction data.
  Methods in enzymology 2023 Du S, Wankowicz SA, Yabukarski F, Doukov T, Herschlag D, Fraser JS
• Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM.
  bioRxiv : the preprint server for biology 2023 Wankowicz SA, Ravikumar A, Sharma S, Riley BT, Raju A, Hogan DW, van den Bedem H, Keedy DA, Fraser JS
• Chemoenzymatic syntheses of fluorine-18-labeled disaccharides from [ 18 F]FDG yield potent sensors of living bacteria in vivo.
  bioRxiv : the preprint server for biology 2023 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, …
• A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication and pathogenesis in vivo.
  bioRxiv : the preprint server for biology 2023 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
• Refinement of Multiconformer Ensemble Models from Multi-temperature X-ray Diffraction Data.
  bioRxiv : the preprint server for biology 2023 Du S, Wankowicz SA, Yabukarski F, Doukov T, Herschlag D, Fraser JS
• Molecular evidence of widespread benzimidazole drug resistance in Ancylostoma caninum from domestic dogs throughout the USA and discovery of a novel β-tubulin benzimidazole resistance mutation.
  PLoS pathogens 2023 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
• DIMPLE: deep insertion, deletion, and missense mutation libraries for exploring protein variation in evolution, disease, and biology.
  Genome biology 2023 Macdonald CB, Nedrud D, Grimes PR, Trinidad D, Fraser JS, Coyote-Maestas W
• Bacteriophages inhibit and evade cGAS-like immune function in bacteria.
  Cell 2023 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
• Context-specific inhibition of translation in mycobacterium.
  Biophysical Journal 2023 Mohamad T. Dandan, James S. Fraser
• Reaction coordinate dependent fibrillar formation of human glutamine synthetase tunes activity.
  Biophysical Journal 2023 Eric R. Greene, Richard Muniz, Angelika Arada, D. John Lee, Daphne Chen, Erin Thompson, Hiroki Yamamura, Justin M. Kollman, James Fraser
• Large language models generate functional protein sequences across diverse families.
  Nature biotechnology 2023 Madani A, Krause B, Greene ER, Subramanian S, Mohr BP, Holton JM, Olmos JL, Xiong C, Sun ZZ, Socher R, Fraser JS, Naik N
• Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2.
  Proceedings of the National Academy of Sciences of the United States of America 2023 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, …
• Molecular-dynamics simulation methods for macromolecular crystallography.
  Acta crystallographica. Section D, Structural biology 2023 Wych DC, Aoto PC, Vu L, Wolff AM, Mobley DL, Fraser JS, Taylor SS, Wall ME
• A language model beats alphafold2 on orphans.
  Nature biotechnology 2022 Michaud JM, Madani A, Fraser JS
• Ensemble-function relationships to dissect mechanisms of enzyme catalysis.
  Science advances 2022 Yabukarski F, Doukov T, Pinney MM, Biel JT, Fraser JS, Herschlag D
• Of problems and opportunities-How to treat and how to not treat crystallographic fragment screening data.
  Protein science : a publication of the Protein Society 2022 Weiss MS, Wollenhaupt J, Correy GJ, Fraser JS, Heine A, Klebe G, Krojer T, Thunissen M, Pearce NM
• Innate type 2 immunity controls hair follicle commensalism by Demodex mites.
  Immunity 2022 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, …
• The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature.
  Science advances 2022 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
• Innate type 2 immunity controls hair follicle commensalism by Demodex mites.
  The Journal of Immunology 2022 Roberto R Ricardo-Gonzalez, Maya E Kotas, Claire O’Leary, Iliana Tenvooren, Diana Marquez, Katelyn Singh, William Damsky, Chang Liao, Andrew Schroeder, Jarish Cohen, Marlys S Fassett, Jinwoo Lee, …
• Ligand binding remodels protein side-chain conformational heterogeneity.
  eLife 2022 Wankowicz SA, de Oliveira SH, Hogan DW, van den Bedem H, Fraser JS
• Accurate positioning of functional residues with robotics-inspired computational protein design.
  Proceedings of the National Academy of Sciences of the United States of America 2022 Krivacic C, Kundert K, Pan X, Pache RA, Liu L, Conchúir SO, Jeliazkov JR, Gray JJ, Thompson MC, Fraser JS, Kortemme T
• Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics.
  Nature structural & molecular biology 2022 Tsai K, Stojkovic V, Lee DJ, Young ID, Szal T, Klepacki D, Vázquez-Laslop N, Mankin AS, Fraser JS, Fujimori DG
• Integration of software tools for integrative modeling of biomolecular systems.
  Journal of structural biology 2022 Hancock M, Peulen TO, Webb B, Poon B, Fraser JS, Adams P, Sali A
• Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance.
  eLife 2022 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
• A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis.
  Nature chemical biology 2021 Jayaraman V, Lee DJ, Elad N, Vimer S, Sharon M, Fraser JS, Tawfik DS
• CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.
  Research square 2021 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, …
• State of the structure address on MET receptor activation by HGF.
  Biochemical Society transactions 2021 Linossi EM, Estevam GO, Oshima M, Fraser JS, Collisson EA, Jura N
• ORACLE reveals a bright future to fight bacteria.
  eLife 2021 Coyote-Maestas W, Fraser JS
• Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
  Science advances 2021 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,…
• Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge.
  Nature methods 2021 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, …
• Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray-derived conformational ensembles.
  Proceedings of the National Academy of Sciences of the United States of America 2020 Yabukarski F, Biel JT, Pinney MM, Doukov T, Powers AS, Fraser JS, Herschlag D
• Genetic interaction mapping informs integrative structure determination of protein complexes.
  Science (New York, N.Y.) 2020 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…
• qFit 3: Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps.
  Protein science : a publication of the Protein Society 2020 Riley BT, Wankowicz SA, de Oliveira SHP, van Zundert GCP, Hogan DW, Fraser JS, Keedy DA, van den Bedem H
• Discovery of allosteric binding sites by crystallographic fragment screening.
  Current opinion in structural biology 2020 Krojer T, Fraser JS, von Delft F
• DNA-binding proteins meet their mismatch.
  Nature 2020 Kundert K, Fraser JS
• Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.
  Science (New York, N.Y.) 2020 Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM, Weckstein AR, Owens TW, Gupta M, Pourmal S, Titus EW, Cakir M, Soucheray M, McGregor…
• Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico.
  Nature communications 2020 Broom A, Rakotoharisoa RV, Thompson MC, Zarifi N, Nguyen E, Mukhametzhanov N, Liu L, Fraser JS, Chica RA
• Synthetic group A streptogramin antibiotics that overcome Vat resistance.
  Nature 2020 Li Q, Pellegrino J, Lee DJ, Tran AA, Chaires HA, 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, Mühle E, Chesneau…
• Expanding the space of protein geometries by computational design of de novo fold families.
  Science (New York, N.Y.) 2020 Pan X, Thompson MC, Zhang Y, Liu L, Fraser JS, Kelly MJS, Kortemme T
• A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.
  Nature 2020 Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, …
• Assessment of the nucleotide modifications in the high-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit.
  Nucleic acids research 2020 Stojkovic V, Myasnikov AG, Young ID, Frost A, Fraser JS, Fujimori DG
• Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals.
  IUCrJ 2020 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, …
• What Will Computational Modeling Approaches Have to Say in the Era of Atomistic Cryo-EM Data?
  Journal of chemical information and modeling 2020 Fraser JS, Lindorff-Larsen K, Bonomi M
• Differences in the chitinolytic activity of mammalian chitinases on soluble and insoluble substrates.
  Protein science : a publication of the Protein Society 2020 Barad BA, Liu L, Diaz RE, Basilio R, Van Dyken SJ, Locksley RM, Fraser JS
• Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein.
  Structural dynamics (Melville, N.Y.) 2019 Wych DC, Fraser JS, Mobley DL, Wall ME
• Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis.
  Proceedings of the National Academy of Sciences of the United States of America 2019 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, …
• Computational design of a modular protein sense-response system.
  Science (New York, N.Y.) 2019 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
• Co-occurring Alterations in the RAS-MAPK Pathway Limit Response to MET Inhibitor Treatment in MET Exon 14 Skipping Mutation-Positive Lung Cancer.
  Clinical cancer research : an official journal of the American Association for Cancer Research 2019 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, …
• Temperature-jump solution X-ray scattering reveals distinct motions in a dynamic enzyme.
  Nature chemistry 2019 Thompson MC, Barad BA, Wolff AM, Sun Cho H, Schotte F, Schwarz DMC, Anfinrud P, Fraser JS
• Synthetic Essentiality of Metabolic Regulator PDHK1 in PTEN-Deficient Cells and Cancers.
  Cell reports 2019 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, …
• Promoting transparency and reproducibility in enhanced molecular simulations.
  Nature methods 2019 PLUMED consortium
• Biomaterials in non-integer dimensions.
  Nature chemistry 2019 Young ID, Fraser JS
• Effects of α-tubulin acetylation on microtubule structure and stability.
  Proceedings of the National Academy of Sciences of the United States of America 2019 Eshun-Wilson L, Zhang R, Portran D, Nachury MV, Toso DB, Löhr T, Vendruscolo M, Bonomi M, Fraser JS, Nogales E
• 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.
  Journal of the American Chemical Society 2019 Hu S, Offenbacher AR, Thompson EM, Gee CL, Wilcoxen J, Carr CAM, Prigozhin DM, Yang V, Alber T, Britt RD, Fraser JS, Klinman JP
• qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps.
  Journal of medicinal chemistry 2018 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
• A Multi-model Approach to Assessing Local and Global Cryo-EM Map Quality.
  Structure (London, England : 1993) 2018 Herzik MA, Fraser JS, Lander GC
• Together scientists and journalists can spot poor preprints.
  Nature 2018 Fraser J, Polka J
• Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance.
  Biology open 2018 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 …
• An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering.
  eLife 2018 Keedy DA, Hill ZB, Biel JT, Kang E, Rettenmaier TJ, Brandão-Neto J, Pearce NM, von Delft F, Wells JA, Fraser JS
• Rescue of conformational dynamics in enzyme catalysis by directed evolution.
  Nature communications 2018 Otten R, Liu L, Kenner LR, Clarkson MW, Mavor D, Tawfik DS, Kern D, Fraser JS
• Bringing diffuse X-ray scattering into focus.
  Current opinion in structural biology 2018 Wall ME, Wolff AM, Fraser JS
• XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction.
  Proceedings of the National Academy of Sciences of the United States of America 2017 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, …
• Allosteric Inhibitors, Crystallography, and Comparative Analysis Reveal Network of Coordinated Movement across Human Herpesvirus Proteases.
  Journal of the American Chemical Society 2017 Acker TM, Gable JE, Bohn MF, Jaishankar P, Thompson MC, Fraser JS, Renslo AR, Craik CS
• 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 central science 2017 Offenbacher AR, Hu S, Poss EM, Carr CAM, Scouras AD, Prigozhin DM, Iavarone AT, Palla A, Alber T, Fraser JS, Klinman JP
• Flexibility and Design: Conformational Heterogeneity along the Evolutionary Trajectory of a Redesigned Ubiquitin.
  Structure (London, England : 1993) 2017 Biel JT, Thompson MC, Cunningham CN, Corn JE, Fraser JS
• Cytidine deaminase efficiency of the lentiviral viral restriction factor APOBEC3C correlates with dimerization.
  Nucleic acids research 2017 Adolph MB, Ara A, Feng Y, Wittkopp CJ, Emerman M, Fraser JS, Chelico L
• Conformational variation of proteins at room temperature is not dominated by radiation damage.
  Journal of synchrotron radiation 2017 Russi S, González A, Kenner LR, Keedy DA, Fraser JS, van den Bedem H
• Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta.
  eLife 2016 Wang RY, Song Y, Barad BA, Cheng Y, Fraser JS, DiMaio F
• From deep TLS validation to ensembles of atomic models built from elemental motions. Addenda and corrigendum.
  Acta crystallographica. Section D, Structural biology 2016 Urzhumtsev A, Afonine PV, Van Benschoten AH, Fraser JS, Adams PD
• SCIENTIFIC COMMUNITY. Preprints for the life sciences.
  Science (New York, N.Y.) 2016 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, …
• Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting.
  eLife 2016 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…
• Measuring and modeling diffuse scattering in protein X-ray crystallography.
  Proceedings of the National Academy of Sciences of the United States of America 2016 Van Benschoten AH, Liu L, Gonzalez A, Brewster AS, Sauter NK, Fraser JS, Wall ME
• Data publication with the structural biology data grid supports live analysis.
  Nature communications 2016 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, …
• CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites.
  Journal of molecular biology 2016 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
• High-density grids for efficient data collection from multiple crystals.
  Acta crystallographica. Section D, Structural biology 2016 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…
• High-resolution structures of the M2 channel from influenza A virus reveal dynamic pathways for proton stabilization and transduction.
  Proceedings of the National Academy of Sciences of the United States of America 2015 Thomaston JL, Alfonso-Prieto M, Woldeyes RA, Fraser JS, Klein ML, Fiorin G, DeGrado WF
• Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit.
  PLoS computational biology 2015 Keedy DA, Fraser JS, van den Bedem H
• Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography.
  eLife 2015 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, …
• EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy.
  Nature methods 2015 Barad BA, Echols N, Wang RY, Cheng Y, DiMaio F, Adams PD, Fraser JS
• From deep TLS validation to ensembles of atomic models built from elemental motions.
  Acta crystallographica. Section D, Biological crystallography 2015 Urzhumtsev A, Afonine PV, Van Benschoten AH, Fraser JS, Adams PD
• Predicting X-ray diffuse scattering from translation-libration-screw structural ensembles.
  Acta crystallographica. Section D, Biological crystallography 2015 Van Benschoten AH, Afonine PV, Terwilliger TC, Wall ME, Jackson CJ, Sauter NK, Adams PD, Urzhumtsev A, Fraser JS
• One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites.
  Chembiochem : a European journal of chemical biology 2015 Fischer M, Shoichet BK, Fraser JS
• 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 Dellus-Gur E, Elias M, Caselli E, Prati F, Salverda ML, de Visser JA, Fraser JS, Tawfik DS
• Lineage-Specific Viral Hijacking of Non-canonical E3 Ubiquitin Ligase Cofactors in the Evolution of Vif Anti-APOBEC3 Activity.
  Cell reports 2015 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, …
• Integrative, dynamic structural biology at atomic resolution--it's about time.
  Nature methods 2015 van den Bedem H, Fraser JS
• Keep on moving: discovering and perturbing the conformational dynamics of enzymes.
  Accounts of chemical research 2014 Bhabha G, Biel JT, Fraser JS
• Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering.
  Proceedings of the National Academy of Sciences of the United States of America 2014 Wall ME, Van Benschoten AH, Sauter NK, Adams PD, Fraser JS, Terwilliger TC
• Discovery and characterization of gut microbiota decarboxylases that can produce the neurotransmitter tryptamine.
  Cell host & microbe 2014 Williams BB, Van Benschoten AH, Cimermancic P, Donia MS, Zimmermann M, Taketani M, Ishihara A, Kashyap PC, Fraser JS, Fischbach MA
• E pluribus unum, no more: from one crystal, many conformations.
  Current opinion in structural biology 2014 Woldeyes RA, Sivak DA, Fraser JS
• Crystal cryocooling distorts conformational heterogeneity in a model Michaelis complex of DHFR.
  Structure (London, England : 1993) 2014 Keedy DA, van den Bedem H, Sivak DA, Petsko GA, Ringe D, Wilson MA, Fraser JS
• Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery.
  Nature chemistry 2014 Fischer M, Coleman RG, Fraser JS, Shoichet BK
• Diffuse X-ray scattering to model protein motions.
  Structure (London, England : 1993) 2014 Wall ME, Adams PD, Fraser JS, Sauter NK
• Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR.
  Proceedings of the National Academy of Sciences of the United States of America 2014 Fenwick RB, van den Bedem H, Fraser JS, Wright PE
• Protein structural ensembles are revealed by redefining X-ray electron density noise.
  Proceedings of the National Academy of Sciences of the United States of America 2013 Lang PT, Holton JM, Fraser JS, Alber T
• From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II.
  Cell 2013 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
• Automated identification of functional dynamic contact networks from X-ray crystallography.
  Nature methods 2013 van den Bedem H, Bhabha G, Yang K, Wright PE, Fraser JS
• From systems to structure: bridging networks and mechanism.
  Molecular cell 2013 Fraser JS, Gross JD, Krogan NJ
• Flexible backbone sampling methods to model and design protein alternative conformations.
  Methods in enzymology 2013 Ollikainen N, Smith CA, Fraser JS, Kortemme T
• CheShift-2 resolves a local inconsistency between two X-ray crystal structures.
  Journal of biomolecular NMR 2012 Vila JA, Sue SC, Fraser JS, Scheraga HA, Dyson HJ
• Systematic functional prioritization of protein posttranslational modifications.
  Cell 2012 Beltrao P, Albanèse V, Kenner LR, Swaney DL, Burlingame A, Villén J, Lim WA, Fraser JS, Frydman J, Krogan NJ
• Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair.
  Proceedings of the National Academy of Sciences of the United States of America 2012 Kapp GT, Liu S, Stein A, Wong DT, Reményi A, Yeh BJ, Fraser JS, Taunton J, Lim WA, Kortemme T
• Accessing protein conformational ensembles using room-temperature X-ray crystallography.
  Proceedings of the National Academy of Sciences of the United States of America 2011 Fraser JS, van den Bedem H, Samelson AJ, Lang PT, Holton JM, Echols N, Alber T
• Mining electron density for functionally relevant protein polysterism in crystal structures.
  Cellular and molecular life sciences : CMLS 2010 Fraser JS, Jackson CJ
• The tumor-associated EpCAM regulates morphogenetic movements through intracellular signaling.
  The Journal of cell biology 2010 Maghzal N, Vogt E, Reintsch W, Fraser JS, Fagotto F
• Automated electron-density sampling reveals widespread conformational polymorphism in proteins.
  Protein science : a publication of the Protein Society 2010 Lang PT, Ng HL, Fraser JS, Corn JE, Echols N, Sales M, Holton JM, Alber T
• Hidden alternative structures of proline isomerase essential for catalysis.
  Nature 2009 Fraser JS, Clarkson MW, Degnan SC, Erion R, Kern D, Alber T
• Immunoglobulin-like domains on bacteriophage: weapons of modest damage?
  Current opinion in microbiology 2007 Fraser JS, Maxwell KL, Davidson AR
• An atypical receiver domain controls the dynamic polar localization of the Myxococcus xanthus social motility protein FrzS.
  Molecular microbiology 2007 Fraser JS, Merlie JP, Echols N, Weisfield SR, Mignot T, Wemmer DE, Zusman DR, Alber T
• Ig-like domains on bacteriophages: a tale of promiscuity and deceit.
  Journal of molecular biology 2006 Fraser JS, Yu Z, Maxwell KL, Davidson AR
• Improving treatment services for substance abusers with comorbid depression.
  The American journal on addictions 2004 Womack S, Compton WM, Dennis M, McCormick S, Fraser J, Horton JC, Spitznagel EL, Cottler LB