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James Fraser, PhD
Chair and Ernest L. Prien Professor
![fraser](/sites/pharmacy.ucsf.edu/files/styles/pharmacy_square_third/public/person/photo/james_fraser_2023_hirez.jpg?itok=gueYywzm×tamp=1700003942)
Phone: +1 415 493-8421
Fax: +1 415 514-9736
600 16th Street, Rm 001
UCSF Box 2240
San Francisco, CA 94158
United States Links
Affiliations
Education programs
UCSF centers, institutes, and research programs
What I do
I coordinate the School’s broad research efforts, aiming to catalyze collaborations across labs, departments, the university, and outside institutions. Additionally, I aim to improve the evaluation of research in hiring and promotion and ensure that our research agenda aligns well with staff and learner career goals.
My research is focused on discovering the macromolecular structure and dynamics of proteins—defining conformational states essential for function and understanding transitions between these states.
I also chair the Department of Bioengineering and Therapeutic Sciences. Details: Administration.
Departmental research area
My research expertise
evolution, protein structure, protein conformational dynamics, x-ray crystallography, nuclear magnetic resonance (NMR), bioengineering
Professional background
Degrees
PhD, Molecular and Cell Biology, University of California, Berkeley, 2010
BSc, Biology, McGill University, 2005
Biography
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.
Research keywords
- evolution
- protein structure
- Protein Conformational Dynamics
- x-ray crystallography
- NMR
- bioengineering
- Protein Conformation
- Chitin
- Tetrahydrofolate Dehydrogenase
- proteins
- X-Ray Diffraction
- Directed Molecular Evolution
- Protein Databases
- Molecular Dynamics Simulation
- Molecular Models
- Crystallography, X-Ray
- Cryoelectron Microscopy
- Child, Orphaned
- Cyclophilin A
- Temperature
- Chitinases
1. | W.H. and W.L. Bragg Prize, International Union of Crystallography, 2020 |
2. | Byers Award in Basic Science, UCSF, 2020 |
3. | Packard Fellow, The David and Lucille Packard Foundation, 2014-2019 |
4. | Searle Scholar, Kinship Foundation, 2014-2017 |
5. | Pew Scholar in the Biomedical Sciences, Pew Charitable Trusts, 2014-2016 |
Publications
Estevam GO, Linossi EM, Rao J, Macdonald CB, Ravikumar A, Chrispens KM, Capra JA, Coyote-Maestas W, Pimentel H, Collisson EA, Jura N, Fraser JS. Mapping kinase domain resistance mechanisms for the MET receptor tyrosine kinase via deep mutational scanning. bioRxiv. 2024 Jul 18. |
Liu F, Mailhot O, Glenn IS, Vigneron SF, Bassim V, Xu X, Fonseca-Valencia K, Smith MS, Radchenko DS, Fraser JS, Moroz YS, Irwin JJ, Shoichet BK. The impact of Library Size and Scale of Testing on Virtual Screening. bioRxiv. 2024 Jul 11. |
Wankowicz SA, Fraser JS. Comprehensive encoding of conformational and compositional protein structural ensembles through the mmCIF data structure. IUCrJ. 2024 Jul 01; 11(Pt 4):494-501. |
Stephanie A Wankowicz, Ashraya Ravikumar, Shivani Sharma, Blake Riley, Akshay Raju, Daniel W Hogan, Jessica Flowers, Henry van den Bedem, Daniel A Keedy, James S Fraser. Automated multiconformer model building for X-ray crystallography and cryo-EM. eLife. 2024 Jun 21; 12. |
Wankowicz SA, Ravikumar A, Sharma S, Riley B, Raju A, Hogan DW, Flowers J, van den Bedem H, Keedy DA, Fraser JS. Automated multiconformer model building for X-ray crystallography and cryo-EM. Elife. 2024 Jun 21; 12. |
Díaz RE, Ecker AK, Correy GJ, Asthana P, Young ID, Faust B, Thompson MC, Seiple IB, Van Dyken S, Locksley RM, Fraser JS. Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase. Elife. 2024 Jun 17; 12. |
Roberto Efraín Díaz, Andrew K Ecker, Galen J Correy, Pooja Asthana, Iris D Young, Bryan Faust, Michael C Thompson, Ian B Seiple, Steven Van Dyken, Richard M Locksley, James S Fraser. Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase. eLife. 2024 Jun 17; 12. |
Rao J, Xin R, Macdonald C, Howard MK, Estevam GO, Yee SW, Wang M, Fraser JS, Coyote-Maestas W, Pimentel H. Rosace: a robust deep mutational scanning analysis framework employing position and mean-variance shrinkage. Genome Biol. 2024 May 24; 25(1):138. |
Estevam GO, Linossi EM, Macdonald CB, Espinoza CA, Michaud JM, Coyote-Maestas W, Collisson EA, Jura N, Fraser JS. Conserved regulatory motifs in the juxtamembrane domain and kinase N-lobe revealed through deep mutational scanning of the MET receptor tyrosine kinase domain. bioRxiv. 2024 May 06. |
Wankowicz SA, Ravikumar A, Sharma S, Riley BT, Raju A, Flowers J, Hogan D, van den Bedem H, Keedy DA, Fraser JS. Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM. bioRxiv. 2024 Apr 30. |
Díaz RE, Ecker AK, Correy GJ, Asthana P, Young ID, Faust B, Thompson MC, Seiple IB, Van Dyken SJ, Locksley RM, Fraser JS. Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase. bioRxiv. 2024 Mar 25. |
Avissar-Whiting M, Belliard F, Bertozzi SM, Brand A, Brown K, Clément-Stoneham G, Dawson S, Dey G, Ecer D, Edmunds SC, Farley A, Fischer TD, Franko M, Fraser JS, Funk K, Ganier C, Harrison M, Hatch A, Hazlett H, Hindle S, Hook DW, Hurst P, Kamoun S, Kiley R, Lacy MM, LaFlamme M, Lawrence R, Lemberger T, Leptin M, Lumb E, MacCallum CJ, Marcum CS, Marinello G, Mendonça A, Monaco S, Neves K, Pattinson D, Polka JK, Puebla I, Rittman M, Royle SJ, Saderi D, Sever R, Shearer K, Spiro JE, Stern B, Taraborelli D, Vale R, Vasquez CG, Waltman L, Watt FM, Weinberg ZY, Williams M. Recommendations for accelerating open preprint peer review to improve the culture of science. PLoS Biol. 2024 Feb; 22(2):e3002502. |
Varkaris A, Pazolli E, Gunaydin H, Wang Q, Pierce L, Boezio AA, Bulku A, DiPietro L, Fridrich C, Frost A, Giordanetto F, Hamilton EP, Harris K, Holliday M, Hunter TL, Iskandar A, Ji Y, Larivée A, LaRochelle JR, Lescarbeau A, Llambi F, Lormil B, Mader MM, Mar BG, Martin I, McLean TH, Michelsen K, Pechersky Y, Puente-Poushnejad E, Raynor K, Rogala D, Samadani R, Schram AM, Shortsleeves K, Swaminathan S, Tajmir S, Tan G, Tang Y, Valverde R, Wehrenberg B, Wilbur J, Williams BR, Zeng H, Zhang H, Walters WP, Wolf BB, Shaw DE, Bergstrom DA, Watters J, Fraser JS, Fortin PD, Kipp DR. Discovery and Clinical Proof-of-Concept of RLY-2608, a First-in-Class Mutant-Selective Allosteric PI3Kα Inhibitor That Decouples Antitumor Activity from Hyperinsulinemia. Cancer Discov. 2024 Feb 08; 14(2):240-257. |
Matthew P. Hancock, James S. Fraser, Andrej Sali. Computing a Bayesian multi-state model of a protein structure from an X-ray diffraction pattern. Biophysical Journal. 2024 Feb 1; 123(3):200a-201a. |
Samuel Hoff, Massimiliano Bonomi, James Fraser, Eric Greene. Extracting conformational heterogeneity from 2D and 3D cryo-EM data. Biophysical Journal. 2024 Feb 1; 123(3):50a-51a. |
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. Product-stabilized filamentation by human glutamine synthetase allosterically tunes activity. Biophysical Journal. 2024 Feb 1; 123(3):352a. |
Rishav Mitra, James Fraser. Role of conformational dynamics in the catalytic mechanism of viral macrodomains. Biophysical Journal. 2024 Feb 1; 123(3):356a-357a. |
Fraser JS, Murcko MA. Structure is beauty, but not always truth. Cell. 2024 Feb 01; 187(3):517-520. |
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. MET variants with activating N-lobe mutations identified in hereditary papillary renal cell carcinomas still require ligand stimulation. bioRxiv. 2023 Nov 07. |
Wolff AM, Nango E, Young ID, Brewster AS, Kubo M, Nomura T, Sugahara M, Owada S, Barad BA, Ito K, Bhowmick A, Carbajo S, Hino T, Holton JM, Im D, O'Riordan LJ, Tanaka T, Tanaka R, Sierra RG, Yumoto F, Tono K, Iwata S, Sauter NK, Fraser JS, Thompson MC. Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography. Nat Chem. 2023 Nov; 15(11):1549-1558. |
Kim DH, Wang Y, Jung H, Field RL, Zhang X, Liu TC, Ma C, Fraser JS, Brestoff JR, Van Dyken SJ. A type 2 immune circuit in the stomach controls mammalian adaptation to dietary chitin. Science. 2023 09 08; 381(6662):1092-1098. |
Taha TY, Suryawanshi RK, Chen IP, Correy GJ, McCavitt-Malvido M, O'Leary PC, Jogalekar MP, Diolaiti ME, Kimmerly GR, Tsou CL, Gascon R, Montano M, Martinez-Sobrido L, Krogan NJ, Ashworth A, Fraser JS, Ott M. A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication in vivo. PLoS Pathog. 2023 08; 19(8):e1011614. |
Sorlin AM, López-Álvarez M, Rabbitt SJ, Alanizi AA, Shuere R, Bobba KN, Blecha J, Sakhamuri S, Evans MJ, Bayles KW, Flavell RR, Rosenberg OS, Sriram R, Desmet T, Nidetzky B, Engel J, Ohliger MA, Fraser JS, Wilson DM. Chemoenzymatic Syntheses of Fluorine-18-Labeled Disaccharides from [18F] FDG Yield Potent Sensors of Living Bacteria In Vivo. J Am Chem Soc. 2023 08 16; 145(32):17632-17642. |
Du S, Wankowicz SA, Yabukarski F, Doukov T, Herschlag D, Fraser JS. Refinement of multiconformer ensemble models from multi-temperature X-ray diffraction data. Methods Enzymol. 2023; 688:223-254. |
Sorlin AM, López-Álvarez M, Rabbitt SJ, Alanizi AA, Shuere R, Bobba KN, Blecha J, Sakhamuri S, Evans MJ, Bayles KW, Flavell RR, Rosenberg OS, Sriram R, Desmet T, Nidetzky B, Engel J, Ohliger MA, Fraser JS, Wilson DM. Chemoenzymatic syntheses of fluorine-18-labeled disaccharides from [ 18 F]FDG yield potent sensors of living bacteria in vivo. bioRxiv. 2023 May 20. |
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. A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication and pathogenesis in vivo. bioRxiv. 2023 May 10. |
Du S, Wankowicz SA, Yabukarski F, Doukov T, Herschlag D, Fraser JS. Refinement of Multiconformer Ensemble Models from Multi-temperature X-ray Diffraction Data. bioRxiv. 2023 May 05. |
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. Molecular evidence of widespread benzimidazole drug resistance in Ancylostoma caninum from domestic dogs throughout the USA and discovery of a novel β-tubulin benzimidazole resistance mutation. PLoS Pathog. 2023 03; 19(3):e1011146. |
Macdonald CB, Nedrud D, Grimes PR, Trinidad D, Fraser JS, Coyote-Maestas W. DIMPLE: deep insertion, deletion, and missense mutation libraries for exploring protein variation in evolution, disease, and biology. Genome Biol. 2023 02 24; 24(1):36. |
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. Bacteriophages inhibit and evade cGAS-like immune function in bacteria. Cell. 2023 02 16; 186(4):864-876.e21. |
Mohamad T. Dandan, James S. Fraser. Context-specific inhibition of translation in mycobacterium. Biophysical Journal. 2023 Feb 1; 122(3):489a. |
Eric R. Greene, Richard Muniz, Angelika Arada, D. John Lee, Daphne Chen, Erin Thompson, Hiroki Yamamura, Justin M. Kollman, James Fraser. Reaction coordinate dependent fibrillar formation of human glutamine synthetase tunes activity. Biophysical Journal. 2023 Feb 1; 122(3):474a. |
Madani A, Krause B, Greene ER, Subramanian S, Mohr BP, Holton JM, Olmos JL, Xiong C, Sun ZZ, Socher R, Fraser JS, Naik N. Large language models generate functional protein sequences across diverse families. Nat Biotechnol. 2023 08; 41(8):1099-1106. |
Gahbauer S, Correy GJ, Schuller M, Ferla MP, Doruk YU, Rachman M, Wu T, Diolaiti M, Wang S, Neitz RJ, Fearon D, Radchenko DS, Moroz YS, Irwin JJ, Renslo AR, Taylor JC, Gestwicki JE, von Delft F, Ashworth A, Ahel I, Shoichet BK, Fraser JS. Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2. Proc Natl Acad Sci U S A. 2023 01 10; 120(2):e2212931120. |
Wych DC, Aoto PC, Vu L, Wolff AM, Mobley DL, Fraser JS, Taylor SS, Wall ME. Molecular-dynamics simulation methods for macromolecular crystallography. Acta Crystallogr D Struct Biol. 2023 Jan 01; 79(Pt 1):50-65. |
Michaud JM, Madani A, Fraser JS. A language model beats alphafold2 on orphans. Nat Biotechnol. 2022 11; 40(11):1576-1577. |
Yabukarski F, Doukov T, Pinney MM, Biel JT, Fraser JS, Herschlag D. Ensemble-function relationships to dissect mechanisms of enzyme catalysis. Sci Adv. 2022 10 14; 8(41):eabn7738. |
Weiss MS, Wollenhaupt J, Correy GJ, Fraser JS, Heine A, Klebe G, Krojer T, Thunissen M, Pearce NM. Of problems and opportunities-How to treat and how to not treat crystallographic fragment screening data. Protein Sci. 2022 09; 31(9):e4391. |
Ricardo-Gonzalez RR, Kotas ME, O'Leary CE, Singh K, Damsky W, Liao C, Arouge E, Tenvooren I, Marquez DM, Schroeder AW, Cohen JN, Fassett MS, Lee J, Daniel SG, Bittinger K, Díaz RE, Fraser JS, Ali N, Ansel KM, Spitzer MH, Liang HE, Locksley RM. Innate type 2 immunity controls hair follicle commensalism by Demodex mites. Immunity. 2022 10 11; 55(10):1891-1908.e12. |
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. The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature. Sci Adv. 2022 May 27; 8(21):eabo5083. |
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, Scott G Daniel, Kyle Bittinger, Roberto Efrain Diaz, James Fraser, Karl Mark Ansel, Matthew Spitzer, Hong-Erh Liang, Richard M Locksley. Innate type 2 immunity controls hair follicle commensalism by Demodex mites. The Journal of Immunology. 2022 May 1; 208(1_Supplement):50.39-50.39. |
Wankowicz SA, de Oliveira SH, Hogan DW, van den Bedem H, Fraser JS. Ligand binding remodels protein side-chain conformational heterogeneity. Elife. 2022 03 21; 11. |
Krivacic C, Kundert K, Pan X, Pache RA, Liu L, Conchúir SO, Jeliazkov JR, Gray JJ, Thompson MC, Fraser JS, Kortemme T. Accurate positioning of functional residues with robotics-inspired computational protein design. Proc Natl Acad Sci U S A. 2022 03 15; 119(11):e2115480119. |
Tsai K, Stojkovic V, Lee DJ, Young ID, Szal T, Klepacki D, Vázquez-Laslop N, Mankin AS, Fraser JS, Fujimori DG. Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics. Nat Struct Mol Biol. 2022 02; 29(2):162-171. |
Hancock M, Peulen TO, Webb B, Poon B, Fraser JS, Adams P, Sali A. Integration of software tools for integrative modeling of biomolecular systems. J Struct Biol. 2022 03; 214(1):107841. |
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. Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance. Elife. 2022 01 11; 11. |
Jayaraman V, Lee DJ, Elad N, Vimer S, Sharon M, Fraser JS, Tawfik DS. A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis. Nat Chem Biol. 2022 02; 18(2):161-170. |
Gupta M, Azumaya CM, Moritz M, Pourmal S, Diallo A, Merz GE, Jang G, Bouhaddou M, Fossati A, Brilot AF, Diwanji D, Hernandez E, Herrera N, Kratochvil HT, Lam VL, Li F, Li Y, Nguyen HC, Nowotny C, Owens TW, Peters JK, Rizo AN, Schulze-Gahmen U, Smith AM, Young ID, Yu Z, Asarnow D, Billesbølle C, Campbell MG, Chen J, Chen KH, Chio US, Dickinson MS, Doan L, Jin M, Kim K, Li J, Li YL, Linossi E, Liu Y, Lo M, Lopez J, Lopez KE, Mancino A, Moss FR, Paul MD, Pawar KI, Pelin A, Pospiech TH, Puchades C, Remesh SG, Safari M, Schaefer K, Sun M, Tabios MC, Thwin AC, Titus EW, Trenker R, Tse E, Tsui TKM, Wang F, Zhang K, Zhang Y, Zhao J, Zhou F, Zhou Y, Zuliani-Alvarez L, QCRG Structural Biology Consortium, Agard DA, Cheng Y, Fraser JS, Jura N, Kortemme T, Manglik A, Southworth DR, Stroud RM, Swaney DL, Krogan NJ, Frost A, Rosenberg OS, Verba KA. CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes. Res Sq. 2021 May 19. |
Linossi EM, Estevam GO, Oshima M, Fraser JS, Collisson EA, Jura N. State of the structure address on MET receptor activation by HGF. Biochem Soc Trans. 2021 04 30; 49(2):645-661. |
Coyote-Maestas W, Fraser JS. ORACLE reveals a bright future to fight bacteria. Elife. 2021 04 15; 10. |
Schuller M, Correy GJ, Gahbauer S, Fearon D, Wu T, Díaz RE, Young ID, Carvalho Martins L, Smith DH, Schulze-Gahmen U, Owens TW, Deshpande I, Merz GE, Thwin AC, Biel JT, Peters JK, Moritz M, Herrera N, Kratochvil HT, QCRG Structural Biology Consortium, Aimon A, Bennett JM, Brandao Neto J, Cohen AE, Dias A, Douangamath A, Dunnett L, Fedorov O, Ferla MP, Fuchs MR, Gorrie-Stone TJ, Holton JM, Johnson MG, Krojer T, Meigs G, Powell AJ, Rack JGM, Rangel VL, Russi S, Skyner RE, Smith CA, Soares AS, Wierman JL, Zhu K, O'Brien P, Jura N, Ashworth A, Irwin JJ, Thompson MC, Gestwicki JE, von Delft F, Shoichet BK, Fraser JS, Ahel I. Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking. Sci Adv. 2021 04; 7(16). |
Lawson CL, Kryshtafovych A, Adams PD, Afonine PV, Baker ML, Barad BA, Bond P, Burnley T, Cao R, Cheng J, Chojnowski G, Cowtan K, Dill KA, DiMaio F, Farrell DP, Fraser JS, Herzik MA, Hoh SW, Hou J, Hung LW, Igaev M, Joseph AP, Kihara D, Kumar D, Mittal S, Monastyrskyy B, Olek M, Palmer CM, Patwardhan A, Perez A, Pfab J, Pintilie GD, Richardson JS, Rosenthal PB, Sarkar D, Schäfer LU, Schmid MF, Schröder GF, Shekhar M, Si D, Singharoy A, Terashi G, Terwilliger TC, Vaiana A, Wang L, Wang Z, Wankowicz SA, Williams CJ, Winn M, Wu T, Yu X, Zhang K, Berman HM, Chiu W. Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge. Nat Methods. 2021 02; 18(2):156-164. |
Yabukarski F, Biel JT, Pinney MM, Doukov T, Powers AS, Fraser JS, Herschlag D. Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray-derived conformational ensembles. Proc Natl Acad Sci U S A. 2020 12 29; 117(52):33204-33215. |
Braberg H, Echeverria I, Bohn S, Cimermancic P, Shiver A, Alexander R, Xu J, Shales M, Dronamraju R, Jiang S, Dwivedi G, Bogdanoff D, Chaung KK, Hüttenhain R, Wang S, Mavor D, Pellarin R, Schneidman D, Bader JS, Fraser JS, Morris J, Haber JE, Strahl BD, Gross CA, Dai J, Boeke JD, Sali A, Krogan NJ. Genetic interaction mapping informs integrative structure determination of protein complexes. Science. 2020 12 11; 370(6522). |
Riley BT, Wankowicz SA, de Oliveira SHP, van Zundert GCP, Hogan DW, Fraser JS, Keedy DA, van den Bedem H. qFit 3: Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps. Protein Sci. 2021 01; 30(1):270-285. |
Krojer T, Fraser JS, von Delft F. Discovery of allosteric binding sites by crystallographic fragment screening. Curr Opin Struct Biol. 2020 12; 65:209-216. |
Kundert K, Fraser JS. DNA-binding proteins meet their mismatch. Nature. 2020 11; 587(7833):199-200. |
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 M, Cakir Z, Jang G, O'Meara MJ, Tummino TA, Zhang Z, Foussard H, Rojc A, Zhou Y, Kuchenov D, Hüttenhain R, Xu J, Eckhardt M, Swaney DL, Fabius JM, Ummadi M, Tutuncuoglu B, Rathore U, Modak M, Haas P, Haas KM, Naing ZZC, Pulido EH, Shi Y, Barrio-Hernandez I, Memon D, Petsalaki E, Dunham A, Marrero MC, Burke D, Koh C, Vallet T, Silvas JA, Azumaya CM, Billesbølle C, Brilot AF, Campbell MG, Diallo A, Dickinson MS, Diwanji D, Herrera N, Hoppe N, Kratochvil HT, Liu Y, Merz GE, Moritz M, Nguyen HC, Nowotny C, Puchades C, Rizo AN, Schulze-Gahmen U, Smith AM, Sun M, Young ID, Zhao J, Asarnow D, Biel J, Bowen A, Braxton JR, Chen J, Chio CM, Chio US, Deshpande I, Doan L, Faust B, Flores S, Jin M, Kim K, Lam VL, Li F, Li J, Li YL, Li Y, Liu X, Lo M, Lopez KE, Melo AA, Moss FR, Nguyen P, Paulino J, Pawar KI, Peters JK, Pospiech TH, Safari M, Sangwan S, Schaefer K, Thomas PV, Thwin AC, Trenker R, Tse E, Tsui TKM, Wang F, Whitis N, Yu Z, Zhang K, Zhang Y, Zhou F, Saltzberg D, QCRG Structural Biology Consortium, Hodder AJ, Shun-Shion AS, Williams DM, White KM, Rosales R, Kehrer T, Miorin L, Moreno E, Patel AH, Rihn S, Khalid MM, Vallejo-Gracia A, Fozouni P, Simoneau CR, Roth TL, Wu D, Karim MA, Ghoussaini M, Dunham I, Berardi F, Weigang S, Chazal M, Park J, Logue J, McGrath M, Weston S, Haupt R, Hastie CJ, Elliott M, Brown F, Burness KA, Reid E, Dorward M, Johnson C, Wilkinson SG, Geyer A, Giesel DM, Baillie C, Raggett S, Leech H, Toth R, Goodman N, Keough KC, Lind AL, Zoonomia Consortium, Klesh RJ, Hemphill KR, Carlson-Stevermer J, Oki J, Holden K, Maures T, Pollard KS, Sali A, Agard DA, Cheng Y, Fraser JS, Frost A, Jura N, Kortemme T, Manglik A, Southworth DR, Stroud RM, Alessi DR, Davies P, Frieman MB, Ideker T, Abate C, Jouvenet N, Kochs G, Shoichet B, Ott M, Palmarini M, Shokat KM, García-Sastre A, Rassen JA, Grosse R, Rosenberg OS, Verba KA, Basler CF, Vignuzzi M, Peden AA, Beltrao P, Krogan NJ. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science. 2020 12 04; 370(6521). |
Broom A, Rakotoharisoa RV, Thompson MC, Zarifi N, Nguyen E, Mukhametzhanov N, Liu L, Fraser JS, Chica RA. Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico. Nat Commun. 2020 09 23; 11(1):4808. |
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 O, Fraser JS, Seiple IB. Synthetic group A streptogramin antibiotics that overcome Vat resistance. Nature. 2020 10; 586(7827):145-150. |
Pan X, Thompson MC, Zhang Y, Liu L, Fraser JS, Kelly MJS, Kortemme T. Expanding the space of protein geometries by computational design of de novo fold families. Science. 2020 08 28; 369(6507):1132-1136. |
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, 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-Ozturk 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. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020 07; 583(7816):459-468. |
Stojkovic V, Myasnikov AG, Young ID, Frost A, Fraser JS, Fujimori DG. 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. |
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. 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. |
Fraser JS, Lindorff-Larsen K, Bonomi M. What Will Computational Modeling Approaches Have to Say in the Era of Atomistic Cryo-EM Data? J Chem Inf Model. 2020 05 26; 60(5):2410-2412. |
Barad BA, Liu L, Diaz RE, Basilio R, Van Dyken SJ, Locksley RM, Fraser JS. Differences in the chitinolytic activity of mammalian chitinases on soluble and insoluble substrates. Protein Sci. 2020 04; 29(4):966-977. |
Wych DC, Fraser JS, Mobley DL, Wall ME. Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein. Struct Dyn. 2019 Nov; 6(6):064704. |
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. 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. |
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. Computational design of a modular protein sense-response system. Science. 2019 11 22; 366(6468):1024-1028. |
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. 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 01 15; 26(2):439-449. |
Thompson MC, Barad BA, Wolff AM, Sun Cho H, Schotte F, Schwarz DMC, Anfinrud P, Fraser JS. Temperature-jump solution X-ray scattering reveals distinct motions in a dynamic enzyme. Nat Chem. 2019 11; 11(11):1058-1066. |
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. Synthetic Essentiality of Metabolic Regulator PDHK1 in PTEN-Deficient Cells and Cancers. Cell Rep. 2019 08 27; 28(9):2317-2330.e8. |
PLUMED consortium. Promoting transparency and reproducibility in enhanced molecular simulations. Nat Methods. 2019 08; 16(8):670-673. |
Young ID, Fraser JS. Biomaterials in non-integer dimensions. Nat Chem. 2019 07; 11(7):599-600. |
Eshun-Wilson L, Zhang R, Portran D, Nachury MV, Toso DB, Löhr T, Vendruscolo M, Bonomi M, Fraser JS, Nogales E. Effects of α-tubulin acetylation on microtubule structure and stability. Proc Natl Acad Sci U S A. 2019 05 21; 116(21):10366-10371. |
Hu S, Offenbacher AR, Thompson EM, Gee CL, Wilcoxen J, Carr CAM, Prigozhin DM, Yang V, Alber T, Britt RD, Fraser JS, Klinman JP. 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. |
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. 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. |
Herzik MA, Fraser JS, Lander GC. A Multi-model Approach to Assessing Local and Global Cryo-EM Map Quality. Structure. 2019 02 05; 27(2):344-358.e3. |
Fraser J, Polka J. Together scientists and journalists can spot poor preprints. Nature. 2018 08; 560(7720):553. |
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. 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). |
Keedy DA, Hill ZB, Biel JT, Kang E, Rettenmaier TJ, Brandão-Neto J, Pearce NM, von Delft F, Wells JA, Fraser JS. An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering. Elife. 2018 06 07; 7. |
Otten R, Liu L, Kenner LR, Clarkson MW, Mavor D, Tawfik DS, Kern D, Fraser JS. Rescue of conformational dynamics in enzyme catalysis by directed evolution. Nat Commun. 2018 04 03; 9(1):1314. |
Wall ME, Wolff AM, Fraser JS. Bringing diffuse X-ray scattering into focus. Curr Opin Struct Biol. 2018 06; 50:109-116. |
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. 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. |
Acker TM, Gable JE, Bohn MF, Jaishankar P, Thompson MC, Fraser JS, Renslo AR, Craik CS. 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. |
Offenbacher AR, Hu S, Poss EM, Carr CAM, Scouras AD, Prigozhin DM, Iavarone AT, Palla A, Alber T, Fraser JS, Klinman JP. 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. |
Biel JT, Thompson MC, Cunningham CN, Corn JE, Fraser JS. Flexibility and Design: Conformational Heterogeneity along the Evolutionary Trajectory of a Redesigned Ubiquitin. Structure. 2017 05 02; 25(5):739-749.e3. |
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 Res. 2017 04 07; 45(6):3378-3394. |
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. J Synchrotron Radiat. 2017 01 01; 24(Pt 1):73-82. |
Wang RY, Song Y, Barad BA, Cheng Y, Fraser JS, DiMaio F. Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta. Elife. 2016 09 26; 5. |
Urzhumtsev A, Afonine PV, Van Benschoten AH, Fraser JS, Adams PD. From deep TLS validation to ensembles of atomic models built from elemental motions. Addenda and corrigendum. Acta Crystallogr D Struct Biol. 2016 09 01; 72(Pt 9):1073-1075. |
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. SCIENTIFIC COMMUNITY. Preprints for the life sciences. Science. 2016 May 20; 352(6288):899-901. |
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. Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting. Elife. 2016 04 25; 5. |
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. Proc Natl Acad Sci U S A. 2016 Apr 12; 113(15):4069-74. |
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. Data publication with the structural biology data grid supports live analysis. Nat Commun. 2016 Mar 07; 7:10882. |
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. CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites. J Mol Biol. 2016 Feb 22; 428(4):709-719. |
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. High-density grids for efficient data collection from multiple crystals. Acta Crystallogr D Struct Biol. 2016 Jan; 72(Pt 1):2-11. |
Thomaston JL, Alfonso-Prieto M, Woldeyes RA, Fraser JS, Klein ML, Fiorin G, DeGrado WF. 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. |
Keedy DA, Fraser JS, van den Bedem H. Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit. PLoS Comput Biol. 2015 Oct; 11(10):e1004507. |
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 Sep 30; 4. |
Barad BA, Echols N, Wang RY, Cheng Y, DiMaio F, Adams PD, Fraser JS. EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy. Nat Methods. 2015 Oct; 12(10):943-6. |
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 Crystallogr D Biol Crystallogr. 2015 Aug; 71(Pt 8):1668-83. |
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 Crystallogr D Biol Crystallogr. 2015 Aug; 71(Pt 8):1657-67. |
Fischer M, Shoichet BK, Fraser JS. One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites. Chembiochem. 2015 Jul 27; 16(11):1560-4. |
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. J Mol Biol. 2015 Jul 17; 427(14):2396-409. |
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. 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. |
van den Bedem H, Fraser JS. Integrative, dynamic structural biology at atomic resolution--it's about time. Nat Methods. 2015 Apr; 12(4):307-18. |
Bhabha G, Biel JT, Fraser JS. Keep on moving: discovering and perturbing the conformational dynamics of enzymes. Acc Chem Res. 2015 Feb 17; 48(2):423-30. |
Wall ME, Van Benschoten 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. Proc Natl Acad Sci U S A. 2014 Dec 16; 111(50):17887-92. |
Williams BB, Van Benschoten AH, Cimermancic P, Donia MS, Zimmermann M, Taketani M, Ishihara A, Kashyap PC, Fraser JS, Fischbach MA. Discovery and characterization of gut microbiota decarboxylases that can produce the neurotransmitter tryptamine. Cell Host Microbe. 2014 Oct 08; 16(4):495-503. |
Woldeyes RA, Sivak DA, Fraser JS. E pluribus unum, no more: from one crystal, many conformations. Curr Opin Struct Biol. 2014 Oct; 28:56-62. |
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 Jun 10; 22(6):899-910. |
Fischer M, Coleman RG, Fraser JS, Shoichet BK. Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery. Nat Chem. 2014 Jul; 6(7):575-83. |
Wall ME, Adams PD, Fraser JS, Sauter NK. Diffuse X-ray scattering to model protein motions. Structure. 2014 Feb 04; 22(2):182-4. |
Fenwick RB, van den Bedem H, Fraser JS, Wright PE. 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. |
Lang PT, Holton JM, Fraser JS, Alber T. 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. |
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. From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II. Cell. 2013 Aug 15; 154(4):775-88. |
van den Bedem H, Bhabha G, Yang K, Wright PE, Fraser JS. Automated identification of functional dynamic contact networks from X-ray crystallography. Nat Methods. 2013 Sep; 10(9):896-902. |
Fraser JS, Gross JD, Krogan NJ. From systems to structure: bridging networks and mechanism. Mol Cell. 2013 Jan 24; 49(2):222-31. |
Ollikainen N, Smith CA, Fraser JS, Kortemme T. Flexible backbone sampling methods to model and design protein alternative conformations. Methods Enzymol. 2013; 523:61-85. |
Vila JA, Sue SC, Fraser JS, Scheraga HA, Dyson HJ. CheShift-2 resolves a local inconsistency between two X-ray crystal structures. J Biomol NMR. 2012 Oct; 54(2):193-8. |
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 Jul 20; 150(2):413-25. |
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. Proc Natl Acad Sci U S A. 2012 Apr 03; 109(14):5277-82. |
Fraser JS, van den Bedem H, Samelson AJ, Lang PT, Holton JM, Echols N, Alber T. 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, Jackson CJ. Mining electron density for functionally relevant protein polysterism in crystal structures. Cell Mol Life Sci. 2011 Jun; 68(11):1829-41. |
Maghzal N, Vogt E, Reintsch W, Fraser JS, Fagotto F. The tumor-associated EpCAM regulates morphogenetic movements through intracellular signaling. J Cell Biol. 2010 Nov 01; 191(3):645-59. |
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 Sci. 2010 Jul; 19(7):1420-31. |
Fraser JS, Clarkson MW, Degnan SC, Erion R, Kern D, Alber T. Hidden alternative structures of proline isomerase essential for catalysis. Nature. 2009 Dec 03; 462(7273):669-73. |
Fraser JS, Maxwell KL, Davidson AR. Immunoglobulin-like domains on bacteriophage: weapons of modest damage? Curr Opin Microbiol. 2007 Aug; 10(4):382-7. |
Fraser JS, Merlie JP, Echols N, Weisfield SR, Mignot T, Wemmer DE, Zusman DR, Alber T. 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, Yu Z, Maxwell KL, Davidson AR. Ig-like domains on bacteriophages: a tale of promiscuity and deceit. J Mol Biol. 2006 Jun 02; 359(2):496-507. |
Womack S, Compton WM, Dennis M, McCormick S, Fraser J, Horton JC, Spitznagel EL, Cottler LB. Improving treatment services for substance abusers with comorbid depression. Am J Addict. 2004 May-Jun; 13(3):295-304. |