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439 entries « 2 of 9 »

2014

Huang, P; Oberdorfer, G; Xu, C; Pei, X Y; Nannenga, B L; Rogers, J M; DiMaio, F; Gonen, T; Luisi, B; Baker, D

High thermodynamic stability of parametrically designed helical bundles Journal Article

Science, 346 , pp. 481-85, 2014.

Abstract | Links | BibTeX

Liu, Yu; Zhang, Xin; Tan, Yun Lei; Bhabha, Gira; Ekiert, Damian C; Kipnis, Yakov; Bjelic, Sinisa; Baker, David; Kelly, Jeffery W

De novo-designed enzymes as small-molecule-regulated fluorescence imaging tags and fluorescent reporters. Journal Article

Journal of the American Chemical Society, 136 , pp. 13102-5, 2014, ISSN: 1520-5126.

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Khoury, George A; Liwo, Adam; Khatib, Firas; Zhou, Hongyi; Chopra, Gaurav; Bacardit, Jaume; Bortot, Leandro O; Faccioli, Rodrigo A; Deng, Xin; He, Yi; Krupa, Pawel; Li, Jilong; Mozolewska, Magdalena A; Sieradzan, Adam K; Smadbeck, James; Wirecki, Tomasz; Cooper, Seth; Flatten, Jeff; Xu, Kefan; Baker, David; Cheng, Jianlin; Delbem, Alexandre C B; Floudas, Christodoulos A; Keasar, Chen; Levitt, Michael; Popovi'c, Zoran; Scheraga, Harold A; Skolnick, Jeffrey; Crivelli, Silvia N

WeFold: a coopetition for protein structure prediction. Journal Article

Proteins, 82 , pp. 1850-68, 2014, ISSN: 1097-0134.

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Griss, Rudolf; Schena, Alberto; Reymond, Luc; Patiny, Luc; Werner, Dominique; Tinberg, Christine E; Baker, David; Johnsson, Kai

Bioluminescent sensor proteins for point-of-care therapeutic drug monitoring Journal Article

Nature chemical biology, 10 , pp. 598-603, 2014, ISSN: 1552-4469.

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Preiswerk, Nathalie; Beck, Tobias; Schulz, Jessica D; Milovn'ik, Peter; Mayer, Clemens; Siegel, Justin B; Baker, David; Hilvert, Donald

Impact of scaffold rigidity on the design and evolution of an artificial Diels-Alderase. Journal Article

Proceedings of the National Academy of Sciences of the United States of America, 111 , pp. 8013-8, 2014, ISSN: 1091-6490.

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Mazor, Ronit; Eberle, Jaime A; Hu, Xiaobo; Vassall, Aaron N; Onda, Masanori; Beers, Richard; Lee, Elizabeth C; Kreitman, Robert J; Lee, Byungkook; Baker, David; King, Chris; Hassan, Raffit; Benhar, Itai; Pastan, Ira

Recombinant immunotoxin for cancer treatment with low immunogenicity by identification and silencing of human T-cell epitopes. Journal Article

Proceedings of the National Academy of Sciences of the United States of America, 111 , pp. 8571-6, 2014, ISSN: 1091-6490.

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Magad'an, Javier G; Altman, Meghan O; Ince, William L; Hickman, Heather D; Stevens, James; Chevalier, Aaron; Baker, David; Wilson, Patrick C; Ahmed, Rafi; Bennink, Jack R; Yewdell, Jonathan W

Biogenesis of Influenza A Virus Hemagglutinin Cross-Protective Stem Epitopes. Journal Article

PLoS pathogens, 10 , pp. e1004204, 2014, ISSN: 1553-7374.

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Procko, Erik; Berguig, Geoffrey Y; Shen, Betty W; Song, Yifan; Frayo, Shani; Convertine, Anthony J; Margineantu, Daciana; Booth, Garrett; Correia, Bruno E; Cheng, Yuanhua; Schief, William R; Hockenbery, David M; Press, Oliver W; Stoddard, Barry L; Stayton, Patrick S; Baker, David

A computationally designed inhibitor of an epstein-barr viral bcl-2 protein induces apoptosis in infected cells. Journal Article

Cell, 157 , pp. 1644-56, 2014, ISSN: 1097-4172.

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Chen, Kuang-Yui M; Sun, Jiaming; Salvo, Jason S; Baker, David; Barth, Patrick

High-resolution modeling of transmembrane helical protein structures from distant homologues. Journal Article

PLoS computational biology, 10 , pp. e1003636, 2014, ISSN: 1553-7358.

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King, Neil P; Bale, Jacob B; Sheffler, William; McNamara, Dan E; Gonen, Shane; Gonen, Tamir; Yeates, Todd O; Baker, David

Accurate design of co-assembling multi-component protein nanomaterials. Journal Article

Nature, 2014, ISSN: 1476-4687.

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Alushin, Gregory M; Lander, Gabriel C; Kellogg, Elizabeth H; Zhang, Rui; Baker, David; Nogales, Eva

High-resolution microtubule structures reveal the structural transitions in αβ-tubulin upon GTP hydrolysis. Journal Article

Cell, 157 , pp. 1117-29, 2014, ISSN: 1097-4172.

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King, Chris; Garza, Esteban N; Mazor, Ronit; Linehan, Jonathan L; Pastan, Ira; Pepper, Marion; Baker, David

Removing T-cell epitopes with computational protein design. Journal Article

Proceedings of the National Academy of Sciences of the United States of America, 2014, ISSN: 1091-6490.

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Ovchinnikov, Sergey; Kamisetty, Hetunandan; Baker, David

Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information. Journal Article

eLife, 3 , pp. e02030, 2014, ISSN: 2050-084X.

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Rajagopalan, Sridharan; Wang, Chu; Yu, Kai; Kuzin, Alexandre P; Richter, Florian; Lew, Scott; Miklos, Aleksandr E; Matthews, Megan L; Seetharaman, Jayaraman; Su, Min; Hunt, John F; Cravatt, Benjamin F; Baker, David

Design of activated serine-containing catalytic triads with atomic-level accuracy Journal Article

Nature chemical biology, 10 , pp. 386-391, 2014, ISSN: 1552-4469.

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Baker, David

Protein folding, structure prediction and design. Journal Article

Biochemical Society transactions, 42 , pp. 225-9, 2014, ISSN: 1470-8752.

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Wang, Yupeng; Khan, Iram F; Boissel, Sandrine; Jarjour, Jordan; Pangallo, Joseph; Thyme, Summer; Baker, David; Scharenberg, Andrew M; Rawlings, David J

Progressive engineering of a homing endonuclease genome editing reagent for the murine X-linked immunodeficiency locus. Journal Article

Nucleic acids research, 2014, ISSN: 1362-4962.

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Liu, Yu; Tan, Yun Lei; Zhang, Xin; Bhabha, Gira; Ekiert, Damian C; Genereux, Joseph C; Cho, Younhee; Kipnis, Yakov; Bjelic, Sinisa; Baker, David; Kelly, Jeffery W

Small molecule probes to quantify the functional fraction of a specific protein in a cell with minimal folding equilibrium shifts. Journal Article

Proceedings of the National Academy of Sciences of the United States of America, 2014, ISSN: 1091-6490.

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Wijma, Hein J; Floor, Robert J; Jekel, Peter A; Baker, David; Marrink, Siewert J; Janssen, Dick B

Computationally designed libraries for rapid enzyme stabilization. Journal Article

Protein engineering, design & selection : PEDS, 27 , pp. 49-58, 2014, ISSN: 1741-0134.

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Correia, Bruno E; Bates, John T; Loomis, Rebecca J; Baneyx, Gretchen; Carrico, Chris; Jardine, Joseph G; Rupert, Peter; Correnti, Colin; Kalyuzhniy, Oleksandr; Vittal, Vinayak; Connell, Mary J; Stevens, Eric; Schroeter, Alexandria; Chen, Man; MacPherson, Skye; Serra, Andreia M; Adachi, Yumiko; Holmes, Margaret A; Li, Yuxing; Klevit, Rachel E; Graham, Barney S; Wyatt, Richard T; Baker, David; Strong, Roland K; Crowe, James E; Johnson, Philip R; Schief, William R

Proof of principle for epitope-focused vaccine design Journal Article

Nature, 2014, ISSN: 1476-4687.

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Shropshire, Tyler D; Reifert, Jack; Rajagopalan, Sridharan; Baker, David; Feinstein, Stuart C; Daugherty, Patrick S

Amyloid β peptide cleavage by kallikrein 7 attenuates fibril growth and rescues neurons from Aβ-mediated toxicity in vitro. Journal Article

Biological chemistry, 395 , pp. 109-18, 2014, ISSN: 1437-4315.

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Thyme, Summer; Baker, David

Redesigning the Specificity of Protein-DNA Interactions with Rosetta. Journal Article

Methods in molecular biology (Clifton, N.J.), 1123 , pp. 265-82, 2014, ISSN: 1940-6029.

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Mao, Binchen; Tejero, Roberto; Baker, David; Montelione, Gaetano Thomas

Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures. Journal Article

Journal of the American Chemical Society, 2014, ISSN: 1520-5126.

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Demers, Jean-Philippe; Habenstein, Birgit; Loquet, Antoine; Vasa, Suresh Kumar; Giller, Karin; Becker, Stefan; Baker, David; Lange, Adam; Sgourakis, Nikolaos G

High-resolution structure of the Shigella type-III secretion needle by solid-state NMR and cryo-electron microscopy. Journal Article

Nature communications, 5 , pp. 4976, 2014, ISSN: 2041-1723.

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Leblanc, Pierre; Moise, Leonard; Luza, Cybelle; Chantaralawan, Kanawat; Lezeau, Lynchy; Yuan, Jianping; Field, Mary; Richer, Daniel; Boyle, Christine; Martin, William D; Fishman, Jordan B; Berg, Eric A; Baker, David; Zeigler, Brandon; Mais, Dale E; Taylor, William; Coleman, Russell; Warren, Shaw H; Gelfand, Jeffrey A; Groot, Anne De S; Brauns, Timothy; Poznansky, Mark C

VaxCelerate II: rapid development of a self-assembling vaccine for Lassa fever. Journal Article

Human vaccines & immunotherapeutics, 10 , pp. 3022-38, 2014, ISSN: 2164-554X.

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2013

Strauch, Eva-Maria; Fleishman, Sarel J; Baker, David

Computational design of a pH-sensitive IgG binding protein Journal Article

Proceedings of the National Academy of Sciences of the United States of America, 2013, ISSN: 1091-6490.

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Fang, Jie; Mehlich, Alexander; Koga, Nobuyasu; Huang, Jiqing; Koga, Rie; Gao, Xiaoye; Hu, Chunguang; Jin, Chi; Rief, Matthias; Kast, Juergen; Baker, David; Li, Hongbin

Forced protein unfolding leads to highly elastic and tough protein hydrogels. Journal Article

Nature communications, 4 , pp. 2974, 2013, ISSN: 2041-1723.

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Boissel, Sandrine; Jarjour, Jordan; Astrakhan, Alexander; Adey, Andrew; Gouble, Agn`es; Duchateau, Philippe; Shendure, Jay; Stoddard, Barry L; Certo, Michael T; Baker, David; Scharenberg, Andrew M

megaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering. Journal Article

Nucleic acids research, 2013, ISSN: 1362-4962.

Abstract | Links | BibTeX

Thyme, Summer B; Boissel, Sandrine J S; Quadri, Arshiya S; Nolan, Tony; Baker, Dean A; Park, Rachel U; Kusak, Lara; Ashworth, Justin; Baker, David

Reprogramming homing endonuclease specificity through computational design and directed evolution. Journal Article

Nucleic acids research, 2013, ISSN: 1362-4962.

Abstract | Links | BibTeX

Cherny, Izhack; Greisen, Per; Ashani, Yacov; Khare, Sagar D; Oberdorfer, Gustav; Leader, Haim; Baker, David; Tawfik, Dan S

Engineering V-type nerve agents detoxifying enzymes using computationally focused libraries Journal Article

ACS chemical biology, 8 , pp. 2394-403, 2013, ISSN: 1554-8937.

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Moretti, Rocco; Fleishman, Sarel J; Agius, Rudi; Torchala, Mieczyslaw; Bates, Paul A; Kastritis, Panagiotis L; Rodrigues, Jo~ao P G L M; Trellet, Mika"el; Bonvin, Alexandre M J J; Cui, Meng; Rooman, Marianne; Gillis, Dimitri; Dehouck, Yves; Moal, Iain; Romero-Durana, Miguel; Perez-Cano, Laura; Pallara, Chiara; Jimenez, Brian; Fernandez-Recio, Juan; Flores, Samuel; Pacella, Michael; Kilambi, Krishna Praneeth; Gray, Jeffrey J; Popov, Petr; Grudinin, Sergei; Esquivel-Rodr'iguez, Juan; Kihara, Daisuke; Zhao, Nan; Korkin, Dmitry; Zhu, Xiaolei; Demerdash, Omar N A; Mitchell, Julie C; Kanamori, Eiji; Tsuchiya, Yuko; Nakamura, Haruki; Lee, Hasup; Park, Hahnbeom; Seok, Chaok; Sarmiento, Jamica; Liang, Shide; Teraguchi, Shusuke; Standley, Daron M; Shimoyama, Hiromitsu; Terashi, Genki; Takeda-Shitaka, Mayuko; Iwadate, Mitsuo; Umeyama, Hideaki; Beglov, Dmitri; Hall, David R; Kozakov, Dima; Vajda, Sandor; Pierce, Brian G; Hwang, Howook; Vreven, Thom; Weng, Zhiping; Huang, Yangyu; Li, Haotian; Yang, Xiufeng; Ji, Xiaofeng; Liu, Shiyong; Xiao, Yi; Zacharias, Martin; Qin, Sanbo; Zhou, Huan-Xiang; Huang, Sheng-You; Zou, Xiaoqin; Velankar, Sameer; Janin, Jo"el; Wodak, Shoshana J; Baker, David

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Journal Article

Proteins, 81 , pp. 1980-7, 2013, ISSN: 1097-0134.

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DiMaio, Frank; Echols, Nathaniel; Headd, Jeffrey J; Terwilliger, Thomas C; Adams, Paul D; Baker, David

Improved low-resolution crystallographic refinement with Phenix and Rosetta. Journal Article

Nature methods, 10 , pp. 1102-4, 2013, ISSN: 1548-7105.

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Song, Yifan; DiMaio, Frank; Wang, Ray Yu-Ruei; Kim, David; Miles, Chris; Brunette, Tj; Thompson, James; Baker, David

High-resolution comparative modeling with RosettaCM. Journal Article

Structure (London, England : 1993), 21 , pp. 1735-42, 2013, ISSN: 1878-4186.

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Niv'on, Lucas G; Bjelic, Sinisa; King, Chris; Baker, David

Automating human intuition for protein design Journal Article

Proteins, 2013, ISSN: 1097-0134.

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Conway, Patrick; Tyka, Michael D; DiMaio, Frank; Konerding, David E; Baker, David

Relaxation of backbone bond geometry improves protein energy landscape modeling. Journal Article

Protein science : a publication of the Protein Society, 2013, ISSN: 1469-896X.

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Bjelic, Sinisa; Kipnis, Yakov; Wang, Ling; Pianowski, Zbigniew; Vorobiev, Sergey; Su, Min; Seetharaman, Jayaraman; Xiao, Rong; Kornhaber, Gregory; Hunt, John F; Tong, Liang; Hilvert, Donald; Baker, David

Exploration of Alternate Catalytic Mechanisms and Optimization Strategies for Retroaldolase Design Journal Article

Journal of molecular biology, 426 , pp. 256-271, 2013, ISSN: 1089-8638.

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Vernon, Robert; Shen, Yang; Baker, David; Lange, Oliver F

Improved chemical shift based fragment selection for CS-Rosetta using Rosetta3 fragment picker. Journal Article

Journal of biomolecular NMR, 57 , pp. 117-27, 2013, ISSN: 1573-5001.

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Cooper, Seth; Khatib, Firas; Baker, David

Increasing public involvement in structural biology Journal Article

Structure (London, England : 1993), 21 , pp. 1482-4, 2013, ISSN: 1878-4186.

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Kamisetty, Hetunandan; Ovchinnikov, Sergey; Baker, David

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era. Journal Article

Proceedings of the National Academy of Sciences of the United States of America, 110 , pp. 15674-9, 2013, ISSN: 1091-6490.

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Procko, Erik; Hedman, Rickard; Hamilton, Keith; Seetharaman, Jayaraman; Fleishman, Sarel J; Su, Min; Aramini, James; Kornhaber, Gregory; Hunt, John F; Tong, Liang; Montelione, Gaetano T; Baker, David

Computational design of a protein-based enzyme inhibitor. Journal Article

Journal of molecular biology, 425 , pp. 3563-75, 2013, ISSN: 1089-8638.

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Tinberg, Christine E; Khare, Sagar D; Dou, Jiayi; Doyle, Lindsey; Nelson, Jorgen W; Schena, Alberto; Jankowski, Wojciech; Kalodimos, Charalampos G; Johnsson, Kai; Stoddard, Barry L; Baker, David

Computational design of ligand-binding proteins with high affinity and selectivity Journal Article

Nature, 501 , pp. 212-6, 2013, ISSN: 1476-4687.

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Mills, Jeremy H; Khare, Sagar D; Bolduc, Jill M; Forouhar, Farhad; Mulligan, Vikram Khipple; Lew, Scott; Seetharaman, Jayaraman; Tong, Liang; Stoddard, Barry L; Baker, David

Computational design of an unnatural amino acid dependent metalloprotein with atomic level accuracy. Journal Article

Journal of the American Chemical Society, 135 , pp. 13393-9, 2013, ISSN: 1520-5126.

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van der Schot, Gijs; Zhang, Zaiyong; Vernon, Robert; Shen, Yang; Vranken, Wim F; Baker, David; Bonvin, Alexandre M J J; Lange, Oliver F

Improving 3D structure prediction from chemical shift data. Journal Article

Journal of biomolecular NMR, 57 , pp. 27-35, 2013, ISSN: 1573-5001.

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Giger, Lars; Caner, Sami; Obexer, Richard; Kast, Peter; Baker, David; Ban, Nenad; Hilvert, Donald

Evolution of a designed retro-aldolase leads to complete active site remodeling. Journal Article

Nature chemical biology, 9 , pp. 494-8, 2013, ISSN: 1552-4469.

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Kim, David E; DiMaio, Frank; Wang, Ray Yu-Ruei; Song, Yifan; Baker, David

One contact for every twelve residues allows robust and accurate topology-level protein structure modeling. Journal Article

Proteins, 2013, ISSN: 1097-0134.

Abstract | Links | BibTeX

DiMaio, Frank; Zhang, Junjie; Chiu, Wah; Baker, David

Cryo-EM model validation using independent map reconstructions Journal Article

Protein science : a publication of the Protein Society, 22 , pp. 865-8, 2013, ISSN: 1469-896X.

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Kiss, Gert; c"um, Nihan Celebi-"Olc; Moretti, Rocco; Baker, David; Houk, K N

Computational enzyme design Journal Article

Angewandte Chemie (International ed. in English), 52 , pp. 5700-25, 2013, ISSN: 1521-3773.

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Jardine, Joseph; Julien, Jean-Philippe; Menis, Sergey; Ota, Takayuki; Kalyuzhniy, Oleksandr; McGuire, Andrew; Sok, Devin; Huang, Po-Ssu; MacPherson, Skye; Jones, Meaghan; Nieusma, Travis; Mathison, John; Baker, David; Ward, Andrew B; Burton, Dennis R; Stamatatos, Leonidas; Nemazee, David; Wilson, Ian A; Schief, William R

Rational HIV immunogen design to target specific germline B cell receptors Journal Article

Science (New York, N.Y.), 340 , pp. 711-6, 2013, ISSN: 1095-9203.

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Bjelic, Sinisa; Niv'on, Lucas G; c c"um, Nihan Celebi-"Olc; Kiss, Gert; Rosewall, Carolyn F; Lovick, Helena M; Ingalls, Erica L; Gallaher, Jasmine Lynn; Seetharaman, Jayaraman; Lew, Scott; Montelione, Gaetano Thomas; Hunt, John Francis; Michael, Forrest Edwin; Houk, K N; Baker, David

Computational design of enone-binding proteins with catalytic activity for the Morita-Baylis-Hillman reaction Journal Article

ACS chemical biology, 8 , pp. 749-57, 2013, ISSN: 1554-8937.

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Geibel, Sebastian; Procko, Erik; Hultgren, Scott J; Baker, David; Waksman, Gabriel

Structural and energetic basis of folded-protein transport by the FimD usher Journal Article

Nature, 496 , pp. 243-6, 2013, ISSN: 1476-4687.

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Bergeron, Julien R C; Worrall, Liam J; Sgourakis, Nikolaos G; DiMaio, Frank; Pfuetzner, Richard A; Felise, Heather B; Vuckovic, Marija; Yu, Angel C; Miller, Samuel I; Baker, David; Strynadka, Natalie C J

A Refined Model of the Prototypical Salmonella SPI-1 T3SS Basal Body Reveals the Molecular Basis for Its Assembly Journal Article

PLoS pathogens, 9 , pp. e1003307, 2013, ISSN: 1553-7374.

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439 entries « 2 of 9 »