Publications

An ILC2-chitinase circuit restores lung homeostasis after epithelial injury
Jung H, Kim DH, Díaz RE, White JM, Rucknagel S, Mosby L, Wang Y, Reddy S, Winkler ES, Hassan AO, Ying B, Diamond MS, Locksley RM, Fraser JS, Van Dyken SJ
Science Immunology, 2024
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Expanding Automated Multiconformer Ligand Modeling to Macrocycles and Fragments
Flowers J, Echols N, Correy G, Jaishankar P, Togo T, Renslo AR, van den Bedem H, Fraser JS, Wankowicz SA
Biorxiv, 2024
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A renewed call for open artificial intelligence in biomedicine
Gitter A, Fraser JS, Gonen T, Patro R, Wayment-Steele HK, Williams A, Haibe-Kains B, Dunbrack RL, Cook C, Kundaje A, Hoffman MM, Carpenter AE, Wankowicz SA, Lindorff-Larsen K
Preprint, 2024
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Conserved regulatory motifs in the juxtamembrane domain and kinase N-lobe revealed through deep mutational scanning of the MET receptor tyrosine kinase domain
Estevam GO, Linossi EM, Macdonald CM, Espinoza CA, Michaud JM, Coyote-Maestas W, Collisson EA, Jura N, Fraser JS
eLife, 2024
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The Mac1 ADP-ribosylhydrolase is a Therapeutic Target for SARS-CoV-2
Suryawanshi RK*, Jaishankar P*, Correy GJ*, Rachman MM*, O’Leary PC*, Taha TY*, Zapatero-Belinchón FJ, McCavitt-Malvido M, Doruk YU, Stevens MGV, Diolati ME, Jogalekar MP, Richards AL, Montano M, Rosecrans J, Matthay M, Togo T, Gonciarz RL, Gopalkrishnan S, Neitz RJ, Krogan NJ, Swaney DL, Shoichet BK, Ott M, Renslo AR, Ashworth A, Fraser JS
Biorxiv, 2024
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Deep mutational scanning of EccD3 reveals the molecular basis of its essentiality in the mycobacterium ESX secretion system
Trinidad DD, Macdonald CB, Rosenberg OS, Fraser JS, Coyote-Maestas W
Biorxiv, 2024
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Extensive exploration of structure activity relationships for the SARS-CoV-2 macrodomain from shape-based fragment merging and active learning
Correy GJ*, Rachman MM*, Togo T, Gahbauer S, Doruk YU, Stevens MGV, Jaishankar P, Kelley B, Goldman B, Schmidt M, Kramer T, Ashworth A, Riley P, Shoichet BK, Renslo AR, Walters WP, Fraser JS
Biorxiv, 2024
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AcrIF11 is a potent CRISPR-specific ADP-ribosyltransferase encoded by phage and plasmid
Chen DF*, Roe LT*, Li Y, Borges AL, Zhang JY, Babbar P, Maji S, Stevens MGV, Correy GJ, Diolaiti ME, Smith DH, Ashworth A, Stroud RM, Kelly MJS, Bondy-Denomy J, Fraser JS
Biorxiv, 2024
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Context-specific inhibition of mitochondrial ribosomes by phenicol and oxazolidinone antibiotics
Bibel B, Raskar T, Couvillion M, Lee M, Kleinman JI, Takeuchi-Tomita N, Churchman LS, Fraser JS, Galonic Fujimori D
Biorxiv, 2024
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Mapping kinase domain resistance mechanisms for the MET receptor tyrosine kinase via deep mutational scanning
Estevam GO, Linossi EM, Rao J, Macdonald CM, Ravikumar A, Chrispens KM, Capra JA, Coyote-Maestas W, Pimentel H, Collisson EA, Jura N, Fraser JS
Biorxiv, 2024
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Ribosomal RNA methylation by GidB modulates discrimination of mischarged tRNA
Bi Z*, Chen YX*, Young ID*, Su HW, Chen Y, Hong JY, Fraser JS, Javid B
Biorxiv, 2024
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The impact of Library Size and Scale of Testing on Virtual Screening
Lui F, Mailhot O, Glenn IS, Vigneron SF, Bassim V, Xu X, Valencia KF, Smith MS, Radchenko DS, Fraser JS, Moroz YS, Irwin JJ, Shoichet BK
Biorxiv, 2024
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Comprehensive Encoding of Conformational and Compositional Protein Structural Ensembles through mmCIF Data Structure
Wankowicz SA, Fraser JS
IUCrJ, 2024
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Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM
Wankowicz SA, Ravikumar A, Sharma S, Riley B, Raju A, Flowers J, Hogan DW, van den Bedem H, Keedy DA, Fraser JS
eLife, 2024
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Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase
Díaz RE, Ecker AK, Correy GJ, Asthana P, Young ID, Faust B, Thompson MC, Seiple IB, Van Dyken SJ, Locksley RM, Fraser JS.
eLife, 2024
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Rosace: a robust deep mutational scanning analysis framework employing position and mean-variance shrinkage
Rao J, Xin R, Macdonald CB, Howard M, Estevam GO, Yee SW, Wang M, Fraser JS, Coyote-Maestas W, Pimentel H
Genome Biology, 2024
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AlphaFold3 Transparency and Reproducibility
Wankowicz SA, Beltrao P, Cravatt B, Dunbrack R, Gitter A, Lindorff-Larsen K, Ovchinnikov S, Polizzi N, Shoichet B, Fraser JS
Preprint, 2024
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Recommendations for accelerating open preprint peer review to improve the culture of science
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.
PLOS Biology, 2024
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Structure is beauty, but not always truth
Fraser JS, Murcko MA
Cell, 2024
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Discovery and clinical proof-of-concept of RLY-2608, a first-in-class mutant-selective allosteric PI3Ka inhibitor that decouples anti-tumor activity from hyperinsulinemia
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.
Cancer Discovery, 2023
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MET variants with activating N-lobe mutations identified in hereditary papillary renal cell carcinomas still require ligand stimulation
Guérin CM, Vinchent A, Damour I, Laratte A, Tellier R, Estevam GO, Meneboo JP, Villenet C, Descarpentries C, Fraser JS, Figeac M, Cortot AB, Rouleau E, Tulasne D
Biorxiv, 2023
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Making sense of chaos: uncovering the mechanisms of conformational entropy
Wankowicz SA, Fraser JS
Preprint, 2023
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Mapping Protein Dynamics at High-Resolution with Temperature-Jump X-ray Crystallography
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
Nature Chemistry, 2023
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A type 2 immune circuit in the stomach controls mammalian adaptation to dietary chitin
Kim D, Wang Y, Jung H, Field RL, Zhang X, Liu T, Ma C, Fraser JS, Brestoff JR, Van Dyken SJ
Science, 2023
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A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication and pathogenesis in vivo
Taha TY*, Suryawanshi RK*, Chen IP*, Correy GJ*, O’Leary PC, Jogalekar MP, McCavitt-Malvido M, Diolaiti M, Kimmerly GR, Tsou CL, Martinez-Sobrido L, Krogan NJ, Ashworth A, Fraser JS, Ott M
PLoS Pathogens, 2023
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Chemoenzymatic syntheses of fluorine-18-labeled disaccharides from [18F]FDG yield potent sensors of living bacteria in vivo
Sorlin A, Alvarez ML, Rabbitt S, Alanizi A, Shuere B, Bobba KN, Blecha J, Sakhamuri S, Evans M, Bayles KJ, Flavell R, Rosenberg O, Sriram R, Desmet T, Nidetzky B, Engel J, Ohliger M, Fraser JS, Wilson DM
JACS, 2023
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Refinement of Multiconformer Ensemble Models from Multi-temperature X-ray Diffraction Data
Du S, Wankowicz SA, Yabukarski F, Doukov T, Herschlag D, Fraser JS
Methods in Enzymology, 2023
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Molecular evidence of widespread benzimidazole drug resistance in Ancylostoma caninum from domestic dogs throughout the USA and discovery of a novel isotype-1 β-tubulin benzimidazole resistance mutation
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
PLoS Pathogens, 2023
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Deep insertion, deletion, and missense mutation libraries for exploring protein variation in evolution, disease, and biology
Macdonald CB, Nedrud D, Rockefeller Grimes P, Trinidad D, Fraser JS, Coyote-Maestas W
Genome Biology, 2023
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Bacteriophages inhibit and evade cGAS-like immune function in bacteria
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
Cell, 2023
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Deep neural language modeling enables functional protein generation across families
Madani A, Krause B*, Greene ER*, Subramanian S, Mohr BP, Holton JM, Olmos Jr. JL, Xiong C, Sun ZZ, Socher R, Fraser JS, Naik N
Nature Biotechnology, 2023
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Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 Macrodomain of SARS-CoV-2
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
PNAS, 2023
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Molecular-Dynamics simulation methods for macromolecular crystallography
Wych DC, Aoto PC, Vu L, Wolff AM, Mobley DL, Fraser JS, Taylor SS, Wall ME
Acta Crystallographica D, 2023
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Fragment-based hit discovery via unsupervised learning of fragment-protein complexes
McCorkindale W, Ahel I, Barr H, Correy GJ, Fraser JS, London N, Schuller M, Shurrush K, Lee AA
Biorxiv, 2022
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Ensemble-function relationships to dissect mechanisms of enzyme catalysis
Yabukarski F, Doukov T, Pinney MM, Biel JT, Fraser JS, Herschlag D
Science Advances, 2022
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Type 2 innate immunity regulates hair follicle homeostasis to control Demodex pathosymbionts
Ricardo-Gonzalez RR, Kotas ME, Tenvooren I, Marquez DM, Fassett MS, Lee J, Daniel SG, Bittinger K, Díaz RE, Fraser JS, Ansel KM, Spitzer MH, Liang HE, Locksley RM
Immunity, 2022
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Of problems and opportunities-How to treat and how to not treat crystallographic fragment screening data
Weiss MS, Wollenhaupt J, Correy GJ, Fraser JS, Heine A, Klebe G, Krojer T, Thunissen M, Pearce NM
Protein Science, 2022
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The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and X-ray diffraction at room temperature
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
Science Advances, 2022
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Ligand binding remodels protein side chain conformational heterogeneity
Wankowicz SA, de Oliveira SHP, Hogan DW, van den Bedem H, Fraser JS
eLife, 2022
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Accurate positioning of functional residues with robotics-inspired computational protein design
Krivacic C*, Kundert K*, Pan X*, Pache RA*, Liu L, Conchúir SO, Jeliazkov JR, Gray JJ, Thompson MC, Fraser JS, Kortemme T
PNAS, 2022
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Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics
Tsai K*, Stojković V*, Lee DJ*, Young ID, Szal T, Vazquez-Laslop N, Mankin AS, Fraser JS, Fujimori DG
Nature Structural and Molecular Biology, 2022
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Integration of software tools for integrative modeling of biomolecular systems
Hancock M, Peulen TO, Webb B, Poon B, Fraser JS, Adams P, Sali A
Journal of Structural Biology, 2022
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A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis
Jayaraman V, Lee DJ, Elad N, Vimer S, Sharon M, Fraser JS, Tawfik DS
Nature Chemical Biology, 2022
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Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance
Tsai K, Stojković V, Noda-Garcia L, Young ID, Myasnikov AG, Kleinman J, Palla A, Floor SN, Frost A, Fraser JS, Tawfik DS, Fujimori DG
eLife, 2022
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CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes
Gupta M*, Azumaya CM*, Moritz M*, Pourmal S*, Diallo A*, Merz GE*, Jang G*, Bouhaddou M*, Fossati*, 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 III FR, Paul MD, Pawar KI, Pelin A, Pospiech Jr. TH, Puchase 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
Biorxiv, 2021
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State of the structure address on MET receptor activation by HGF
Linossi EM, Estevam GO, Oshima M, Fraser JS, Collisson EA, Jura N
Biochemical Society Transactions, 2021
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Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking
Schuller M*, Correy GJ*, Gahbauer S*, Fearon D*, Wu T, Díaz RE, Young ID, Carvalho Martins L, Smith DS, Schulze-Gahmen U, Owens TW, Deshpande I, Merz GE, Thwin AC, Biel JT, Peters JK, Mortiz M, Herrera N, Kratochvil HT, QCRG Structural Biology Consortium, Aimon A, Bennett MJ, Brandao Neto J, Cohen EA, Dias A, Douangamath A, Dunnett L, Fedorov O, Ferla PM, Fuchs M, Gorrie-Stone JT, Holton MJ, Johnson GM, Krojer T, Meigs G, Powell JA, Rack J, Rangel LV, Russi S, Skyner ER, Smith AC, Soares SA, Wierman LJ, Zhu K, O’Brien P, Jura N, Ashworth A, Irwin J, Thompson MC, Gestwicki JE, von Delft F, Shoichet BK, Fraser JS, Ahel I
Science Advances, 2021
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Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge
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, Jr. Herzik MA, Hoh SW, Hou J, Hung L, 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
Nature Methods, 2021
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qFit 3: Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps
Riley BT, Wankowicz SA, de Oliveira SHP, van Zundert GCP, Hogan DW, Fraser JS, Keedy DA, van den Bedem H
Protein Science, 2021
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Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray–derived conformational ensembles
Yabukarski F, Biel JT, Pinney MM, Doukov T, Powers AS, Fraser JS, Herschlag D
PNAS, 2020
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Genetic interaction mapping informs integrative structure determination of protein complexes
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
Science, 2020
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Discovery of allosteric binding sites by crystallographic fragment screening
Krojer T, Fraser JS, von Delft F
Current Opinions in Structural Biology, 2020
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Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms
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 3rd, Nguyen P, Paulino J, Pawar KI, Peters JK, Pospiech TH Jr, 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
Science, 2020
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Synthetic group A streptogramin antibiotics that overcome Vat resistance
Li Q*, Pellegrino J*, Lee DJ, Tran AA, Chaires HC, 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
Nature, 2020
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Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico
Broom A*, Rakotoharisoa RV*, Thompson MC, Zarifi N, Nguyen E, Mukhametzhanov N, Liu L, Fraser JS, Chica RA
Nature Communications, 2020
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Expanding the space of protein geometries by computational design of ​de novo fold families
Pan X, Thompson MC, Zhang Y, Liu L, Fraser JS, Kelly MJS, Kortemme T
Science, 2020
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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
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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
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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
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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
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Ensemble refinement produces consistent R-free values but smaller ensemble sizes than previously reported
Wankowicz SA, Fraser JS
Computational Crystallography Newsletter, 2020
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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
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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
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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
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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
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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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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
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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
Journal of Medicinal Chemistry, 2018
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Model selection for biological crystallography
Babcock NS, Keedy DA, Fraser JS, Sivak DA
Biorxiv, 2018
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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
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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
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Bringing diffuse X-ray scattering into focus
Wall ME, Wolff AM, Fraser JS
Current Opinion in Structural Biology, 2018
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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
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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
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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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Preprints for the life sciences
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
Science, 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
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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
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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, Chatterjee R, Degrado WF, Fraser JS, Ibrahim M, Kern J, Kobilka BK, Kruse AC, Larsson KM, Lemke HT, Lyubimov AY, Manglik A, McPhillips SE, Norgren E, Pang SS, Soltis SM, Song J, Thomaston J, Tsai Y, Weis WI, Woldeyes RA, Yachandra V, Yano J, Zouni A, Cohen AE
Acta Crystallographica D, 2016
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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
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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
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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
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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
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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
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E pluribus unum, no more: from one crystal, many conformations
Woldeyes RA, Sivak DA, Fraser JS
Current Opinion in Structural Biology, 2014
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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
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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
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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
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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
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Flexible backbone sampling methods to model and design protein alternative conformations
Ollikainen N, Smith CA, Fraser JS, Kortemme T
Methods in Enzymology, 2013
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From systems to structure: bridging networks and mechanism
Fraser JS, Gross JD, Krogan NJ
Nature Methods, 2013
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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
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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
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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
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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
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Mining electron density for functionally relevant protein polysterism in crystal structures
Fraser JS, Jackson CJ
Cellular and Molecular Life Sciences, 2010
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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
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Hidden alternative structures of proline isomerase essential for catalysis
Fraser JS, Clarkson MW, Degnan SC, Erion R, Kern D, Alber T
Nature, 2009
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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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