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460 entries « 2 of 10 »

2015

Feng, J; Jester, BW; Tinberg, CE; Mandell, DJ; Antunes, MS; Chari, R; Morey, KJ; Rios, X; Medford, JI; Church, GM; Fields, S; Baker, D

A general strategy to construct small molecule biosensors in eukaryotes Journal Article

Elife, 2015.

Abstract | Links | BibTeX

Doyle, L; Hallinan, J; Bolduc, J; Parmeggiani, F; Baker, D; Stoddard, BL; Bradley, P

Rational design of α-helical tandem repeat proteins with closed architectures Journal Article

Nature, 528(7583) , pp. 585-8, 2015.

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Brunette, TJ; Parmeggiani, F; Huang, PS; Bhabha, G; Ekiert, DC; Tsutakawa, SE; Hura, GL; Tainer, JA; Baker, D

Exploring the repeat protein universe through computational protein design Journal Article

Nature, 528(7583) , pp. 580-4, 2015.

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Taylor, ND; Garruss, AS; Moretti, R; Chan, S; Arbing, MA; Cascio, D; Rogers, JK; Isaacs, FJ; Kosuri, S; Baker, D; Fields, S; Church, GM; Raman, S

Engineering an allosteric transcription factor to respond to new ligands Journal Article

Nature Methods, 2015.

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Ovchinnikov, S; Kim, DE; Wang, RY; Liu, Y; DiMaio, F; Baker, D

Improved de novo structure prediction in CASP11 by incorporating Co-evolution information into rosetta Journal Article

Proteins, 2015.

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King, IC; Gleixner, J; Doyle, L; Kuzin, A; Hunt, JF; Xiao, R; Montelione, GT; Stoddard, BL; DiMaio, F; Baker, D

Precise assembly of complex beta sheet topologies from de novo designed building blocks Journal Article

Elife, 2015.

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Goldsmith, M; Eckstein, S; Ashani, Y; Greisen, Jr P; Leader, H; Sussman, JL; Aggarwal, N; Ovchinnikov, S; Tawfik, DS; Baker, D; Thiermann, H; Worek, F

Catalytic efficiencies of directly evolved phosphotriesterase variants with structurally different organophosphorus compounds in vitro Journal Article

Archives of Toxicology, 2015.

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Huang, PS; Feldmeier, K; Parmeggiani, F; Velasco, DA Fernandez; Höcker, B; Baker, D

De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy Journal Article

Nature Chemical Biology, 12(1) , pp. 29-34, 2015.

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Lin YR Koga N, Tatsumi-Koga Liu Clouser AF Montelione GT Baker R G D

Control over overall shape and size in de novo designed proteins Journal Article

Proc Natl Acad Sci U S A., pp. E5478-85, 2015.

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Holstein, Carly A; Chevalier, Aaron; Bennett, Steven; Anderson, Caitlin E; Keniston, Karen; Olsen, Cathryn; Li, Bing; Bales, Brian; Moore, David R; Fu, Elain; Baker, David; Yager, Paul

Immobilizing affinity proteins to nitrocellulose: a toolbox for paper-based assay developers. Journal Article

Analytical and bioanalytical chemistry, 2015, ISSN: 1618-2650.

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S Ovchinnikov L Kinch, Park Liao Pei DE Kim Kamisetty NV Grishin Baker H Y J H D

Large-scale determination of previously unsolved protein structures using evolutionary information Journal Article

eLife, 2015.

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Wolf, Clancey; Siegel, Justin B; Tinberg, Christine; Camarca, Alessandra; Gianfrani, Carmen; Paski, Shirley; Guan, Rongjin; Montelione, Gaetano T; Baker, David; Pultz, Ingrid S

Engineering of Kuma030: a gliadin peptidase that rapidly degrades immunogenic gliadin peptides in gastric conditions. Journal Article

Journal of the American Chemical Society, 2015, ISSN: 1520-5126.

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Bale, Jacob B; Park, Rachel U; Liu, Yuxi; Gonen, Shane; Gonen, Tamir; Cascio, Duilio; King, Neil P; Yeates, Todd O; Baker, David

Structure of a designed tetrahedral protein assembly variant engineered to have improved soluble expression Journal Article

Protein science : a publication of the Protein Society, 2015, ISSN: 1469-896X.

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Gonen, Shane; DiMaio, Frank; Gonen, Tamir; Baker, David

Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces Journal Article

Science (New York, N.Y.), 348 , pp. 1365-8, 2015, ISSN: 1095-9203.

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Park, Hahnbeom; DiMaio, Frank; Baker, David

The origin of consistent protein structure refinement from structural averaging. Journal Article

Structure (London, England : 1993), 23 , pp. 1123-8, 2015, ISSN: 1878-4186.

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Siegel, Justin B; Smith, Amanda Lee; Poust, Sean; Wargacki, Adam J; Bar-Even, Arren; Louw, Catherine; Shen, Betty W; Eiben, Christopher B; Tran, Huu M; Noor, Elad; Gallaher, Jasmine L; Bale, Jacob; Yoshikuni, Yasuo; Gelb, Michael H; Keasling, Jay D; Stoddard, Barry L; Lidstrom, Mary E; Baker, David

Computational protein design enables a novel one-carbon assimilation pathway Journal Article

Proceedings of the National Academy of Sciences of the United States of America, 2015, ISSN: 1091-6490.

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DiMaio, Frank; Song, Yifan; Li, Xueming; Brunner, Matthias J; Xu, Chunfu; Conticello, Vincent; Egelman, Edward; Marlovits, Thomas C; Cheng, Yifan; Baker, David

Atomic-accuracy models from 4.5-r A cryo-electron microscopy data with density-guided iterative local refinement. Journal Article

Nature methods, 2015, ISSN: 1548-7105.

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Wang, Ray Yu-Ruei; Kudryashev, Mikhail; Li, Xueming; Egelman, Edward H; Basler, Marek; Cheng, Yifan; Baker, David; DiMaio, Frank

De novo protein structure determination from near-atomic-resolution cryo-EM maps. Journal Article

Nature methods, 2015, ISSN: 1548-7105.

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Rossi, Paolo; Shi, Lei; Liu, Gaohua; Barbieri, Christopher M; Lee, Hsiau-Wei; Grant, Thomas D; Luft, Joseph R; Xiao, Rong; Acton, Thomas B; Snell, Edward H; Montelione, Gaetano T; Baker, David; Lange, Oliver F; Sgourakis, Nikolaos G

A hybrid NMR/SAXS-based approach for discriminating oligomeric protein interfaces using Rosetta Journal Article

Proteins, 83 , pp. 309-17, 2015, ISSN: 1097-0134.

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Pearson, Aaron D; Mills, Jeremy H; Song, Yifan; Nasertorabi, Fariborz; Han, Gye Won; Baker, David; Stevens, Raymond C; Schultz, Peter G

Transition states. Trapping a transition state in a computationally designed protein bottle. Journal Article

Science (New York, N.Y.), 347 , pp. 863-7, 2015, ISSN: 1095-9203.

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Egelman, E H; Xu, C; DiMaio, F; Magnotti, E; Modlin, C; Yu, X; Wright, E; Baker, D; Conticello, V P

Structural plasticity of helical nanotubes based on coiled-coil assemblies. Journal Article

Structure (London, England : 1993), 23 , pp. 280-9, 2015, ISSN: 1878-4186.

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Morag, Omry; Sgourakis, Nikolaos G; Baker, David; Goldbourt, Amir

The NMR-Rosetta capsid model of M13 bacteriophage reveals a quadrupled hydrophobic packing epitope Journal Article

Proceedings of the National Academy of Sciences of the United States of America, 112 , pp. 971-6, 2015, ISSN: 1091-6490.

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Vittal, Vinayak; Shi, Lei; Wenzel, Dawn M; Scaglione, Matthew K; Duncan, Emily D; Basrur, Venkatesha; Elenitoba-Johnson, Kojo S J; Baker, David; Paulson, Henry L; Brzovic, Peter S; Klevit, Rachel E

Intrinsic disorder drives N-terminal ubiquitination by Ube2w Journal Article

Nature Chemical Biology, 11 , pp. 83-9, 2015, ISSN: 1552-4469.

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Park, Keunwan; Shen, Betty W; Parmeggiani, Fabio; Huang, Po-Ssu; Stoddard, Barry L; Baker, David

Control of repeat-protein curvature by computational protein design. Journal Article

Nature structural & molecular biology, 2015, ISSN: 1545-9985.

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Bergeron, Julien R C; Worrall, Liam J; De, Soumya; Sgourakis, Nikolaos G; Cheung, Adrienne H; Lameignere, Emilie; Okon, Mark; Wasney, Gregory A; Baker, David; McIntosh, Lawrence P; Strynadka, Natalie C J

The modular structure of the inner-membrane ring component PrgK facilitates assembly of the type III secretion system basal body Journal Article

Structure (London, England : 1993), 23 , pp. 161-72, 2015, ISSN: 1878-4186.

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2014

Thyme, Summer B; Song, Yifan; Brunette, Tj; Szeto, Mindy D; Kusak, Lara; Bradley, Philip; Baker, David

Massively parallel determination and modeling of endonuclease substrate specificity Journal Article

Nucleic Acids Research, 42 , pp. 13839-52, 2014, ISSN: 1362-4962.

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Parmeggiani, Fabio; Huang, Po-Ssu; Vorobiev, Sergey; Xiao, Rong; Park, Keunwan; Caprari, Silvia; Su, Min; Seetharaman, Jayaraman; Mao, Lei; Janjua, Haleema; Montelione, Gaetano T; Hunt, John; Baker, David

A General Computational Approach for Repeat Protein Design. Journal Article

Journal of molecular biology, 2014, ISSN: 1089-8638.

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Liu, Daniel S; Niv'on, Lucas G; Richter, Florian; Goldman, Peter J; Deerinck, Thomas J; Yao, Jennifer Z; Richardson, Douglas; Phipps, William S; Ye, Anne Z; Ellisman, Mark H; Drennan, Catherine L; Baker, David; Ting, Alice Y

Computational design of a red fluorophore ligase for site-specific protein labeling in living cells. Journal Article

Proceedings of the National Academy of Sciences of the United States of America, 111 , pp. E4551-9, 2014, ISSN: 1091-6490.

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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.

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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.

Abstract | Links | BibTeX

460 entries « 2 of 10 »