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434 entries « 1 of 9 »

2017

I, Anishchenko; S, Ovchinnikov; H, Kamisetty; D, Baker

Origins of coevolution between residues distant in protein 3D structures. Journal Article

Proceedings of the National Academy of Sciences, 114 (34), pp. 9122-9127, 2017.

Abstract | Links | BibTeX

Rocklin, GJ; Chidyausiku, TM; Goreshnik, I; Ford, A; Houliston, S; Lemak, A; Carter, L; Ravichandran, R; Mulligan, VK; Chevalier, A; Arrowsmith, CH; Baker, D

Global analysis of protein folding using massively parallel design, synthesis, and testing Journal Article

Science, 357 , pp. 168-175, 2017.

Abstract | Links | BibTeX

Strauch, Eva-Maria ; Bernard, Steffen M; La, David ; Bohn, Alan J; Lee, Peter S; Anderson, Caitlin E; Nieusma, Travis ; Holstein, Carly A; Garcia, Natalie K; Hooper, Kathryn A; Ravichandran, Rashmi ; Nelson, Jorgen W; Sheffler, William ; Bloom, Jesse D; Lee, Kelly K; Ward, Andrew B; Yager, Paul ; Fuller, Deborah H; Wilson, Ian A; Baker, David

Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site Journal Article

Nature Biotechnology, [Epub ahead of print] , 2017, ISSN: 1546-1696.

Abstract | Links | BibTeX

CY, Janda; LT, Dang; C, You; J, Chang; de W, Lau; ZA, Zhong; KS, Yan; O, Marecic; D, Siepe; X, Li; JD, Moody; BO, Williams; H, Clevers; J, Piehler; D, Baker; CJ, Kuo; KC, Garcia

Surrogate Wnt agonists that phenocopy canonical Wnt and β-catenin signalling. Journal Article

Nature, 545 (7653), pp. 234-237, 2017.

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Marcos, Enrique ; Basanta, Benjamin ; Chidyausiku, Tamuka M; Tang, Yuefeng ; Oberdorfer, Gustav ; Liu, Gaohua ; Swapna, G V T; Guan, Rongjin ; Silva, Daniel-Adriano ; Dou, Jiayi ; Pereira, Jose Henrique ; Xiao, Rong ; Sankaran, Banumathi ; Zwart, Peter H; Montelione, Gaetano T; Baker, David

Principles for designing proteins with cavities formed by curved β sheets Journal Article

Science, 355 (6321), pp. 201–206, 2017, ISSN: 0036-8075.

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Ovchinnikov, Sergey; Park, Hahnbeom; Varghese, Neha; Huang, Po-Ssu; Pavlopoulos, Georgios A; Kim, David E; Kamisetty, Hetunandan; Kyrpides, Nikos C; Baker, David

Protein structure determination using metagenome sequence data Journal Article

Science, 355 (6322), pp. 294–298, 2017, ISSN: 0036-8075.

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2016

Mills, Jeremy H; Sheffler, William; Ener, Maraia E; Almhjell, Patrick J; Oberdorfer, Gustav; Pereira, José Henrique; Parmeggiani, Fabio; Sankaran, Banumathi; Zwart, Peter H; Baker, David

Computational design of a homotrimeric metalloprotein with a trisbipyridyl core Journal Article

PNAS, 113 (52), pp. 15012-15017, 2016.

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Berger S Procko E, Margineantu Lee EF Shen BW Zelter Silva DA Chawla Herold MJ Garnier JM Johnson MacCoss MJ Lessene Davis TN Stayton PS Stoddard BL Fairlie WD Hockenbery DM Baker D A K R G D

Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer Journal Article

Elife, 2016.

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Huang, Po-Ssu; Boyken, Scott E; Baker, David

The coming of age of de novo protein design Journal Article

Nature, 537 , pp. 320-327, 2016.

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Bhardwaj, Gaurav; Mulligan, Vikram Khipple; Bahl, Christopher D; Gilmore, Jason M; Harvey, Peta J; Cheneval, Olivier; Buchko, Garry W; Pulavarti, Surya V S R K; Kaas, Quentin; Eletsky, Alexander; Huang, Po-Ssu; Johnsen, William A; Greisen, Per Jr; Rocklin, Gabriel J; Song, Yifan; Linsky, Thomas W; Watkins, Andrew; Rettie, Stephen A; Xianzhong Xu, Lauren Carter P; Bonneau, Richard; Olson, James M; Coutsias, Evangelos; Correnti, Colin E; Szyperski, Thomas; Craik, David J; Baker, David

Accurate de novo design of hyperstable constrained peptides Journal Article

Nature, 2016.

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Bale, Jacob B; Gonen, Shane; Liu, Yuxi; Sheffler, William; Ellis, Daniel; Thomas, Chantz; Cascio, Duilio; Yeates, Todd O; Gonen, Tamir; King, Neil P; Baker, David

Accurate design of megadalton-scale two-component icosahedral protein complexes Journal Article

Science, 353 (6297), pp. 389-394, 2016.

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Hsia, Yang; Bale, Jacob B; Gonen, Shane; Shi, Dan; Sheffler, William; Fong, Kimberly K; Nattermann, ; Xu, Chunfu; Huang, Po-Ssu; Ravichandran, Rashmi; Yi, Sue; Davis, Trisha N; Gonen, Tamir; King, Neil P; Baker, David

Design of a hyperstable 60-subunit protein icosahedron Journal Article

Nature, 2016.

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Klein J. C., Lajoie Schwartz Strauch Nelson Baker & Shendure M J J J E -M J D J

Multiplex pairwise assembly of array-derived DNA oligonucleotides Journal Article

Nucleic Acids Research, 44 (5), pp. e43, 2016.

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

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

Nature Methods, 13 (2), pp. 177-83, 2016.

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Boyken, Scott E; Chen, Zibo; Groves, Benjamin; Langan, Robert A; Oberdorfer, Gustav; Ford, Alex; Gilmore, Jason M; Xu, Chunfu; DiMaio, Frank; Pereira, Jose Henrique; Sankaran, Banumathi; Seelig, Georg; Zwart, Peter H; Baker, David

De novo design of protein homo-oligomers with modular hydrogen-bond network–mediated specificity Journal Article

Science, 352 (6286), pp. 680–687, 2016, ISSN: 0036-8075.

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Ovchinnikov, Sergey ; Park, Hahnbeom ; Kim, David E; Liu, Yuan ; Wang, Ray Yu-Ruei ; Baker, David

Structure prediction using sparse simulated NOE restraints with Rosetta in CASP11 Journal Article

Proteins: Structure, Function, and Bioinformatics, pp. n/a–n/a, 2016, ISSN: 1097-0134.

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Basanta, Benjamin; Chan, Kui K; Barth, Patrick; King, Tiffany; Sosnick, Tobin R; Hinshaw, James R; Liu, Gaohua; Everett, John K; Xiao, Rong; Montelione, Gaetano T; Baker, David

Introduction of a polar core into the de novo designed protein Top7 Journal Article

Protein Science, pp. n/a–n/a, 2016, ISSN: 1469-896X.

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Treants, Merika; Jorgen, Nelson; Aaron, Chevalier; Michael, Koday; Hannah, Kalinoski; Lance, Stewart; Lauren, Carter; Travis, Nieusma; S., Lee Peter; B., Ward Andrew; A., Wilson Ian; Ashley, Dagley; F., Smee Donald; David, Baker; Koday, Fuller Deborah Heydenburg

A Computationally Designed Hemagglutinin Stem-Binding Protein Provides In Vivo Protection from Influenza Independent of a Host Immune Response Journal Article

PLoS Pathog, 12 (2), pp. 1-23, 2016.

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Garcia, Kristen E; Babanova, Sofia; Scheffler, William; Hans, Mansij; Baker, David; Atanassov, Plamen; Banta, Scott

Designed protein aggregates entrapping carbon nanotubes for bioelectrochemical oxygen reduction Journal Article

Biotechnology and Bioengineering, pp. n/a–n/a, 2016, ISSN: 1097-0290.

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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.

Abstract | Links | BibTeX

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.

Abstract | Links | BibTeX

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.

Abstract | Links | BibTeX

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.

Abstract | Links | BibTeX

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.

Abstract | Links | BibTeX

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.

Abstract | Links | BibTeX

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.

Abstract | Links | BibTeX

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.

Abstract | Links | BibTeX

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.

Abstract | Links | BibTeX

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.

Abstract | Links | BibTeX

434 entries « 1 of 9 »