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461 entries « 1 of 10 »

2019

Brian D. Weitzner Yakov Kipnis, Gerard Daniel Donald Hilvert David Baker A

A computational method for design of connected catalytic networks in proteins Journal Article

Protein Science, 2019.

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Langan, Robert A; Boyken, Scott E; Ng, Andrew H; Samson, Jennifer A; Dods, Galen ; Westbrook, Alexandra M; Nguyen, Taylor H; Lajoie, Marc J; Chen, Zibo ; Berger, Stephanie ; Mulligan, Vikram Khipple ; Dueber, John E; Novak, Walter R P; El-Samad, Hana ; Baker, David

De novo design of bioactive protein switches Journal Article

Nature, 2019.

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Ng, Andrew H; Nguyen, Taylor H; Gómez-Schiavon, Mariana ; Dods, Galen ; Langan, Robert A; Boyken, Scott E; Samson, Jennifer A; Waldburger, Lucas M; Dueber, John E; Baker, David ; El-Samad, Hana

Modular and tunable biological feedback control using a de novo protein switch Journal Article

Nature, 2019.

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Park, Hahnbeom; Lee, Gyu Rie; Kim, David E; Anishchanka, Ivan; Cong, Qian; Baker, David

High‐accuracy refinement using Rosetta in CASP13 Journal Article

Proteins, 2019.

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Cong, Qian; Anishchenko, Ivan; Ovchinnikov, Sergey; Baker, David

Protein interaction networks revealed by proteome coevolution Journal Article

Science, 2019.

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Pyles, Harley; Zhang, Shuai; Yoreo, James De J; Baker, David

Controlling protein assembly on inorganic crystals through designed protein interfaces Journal Article

Nature, 2019.

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Koepnick, Brian ; Flatten, Jeff ; Husain, Tamir ; Ford, Alex ; Silva, Daniel-Adriano ; Bick, Matthew J; Bauer, Aaron ; Liu, Gaohua ; Ishida, Yojiro ; Boykov, Alexander ; Estep, Roger D; Kleinfelter, Susan ; Nørgård-Solano, Toke ; Wei, Linda ; Players, Foldit ; Montelione, Gaetano T; DiMaio, Frank ; Popović, Zoran ; Khatib, Firas ; Cooper, Seth ; Baker, David

De novo protein design by citizen scientists Journal Article

Nature, 2019.

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Mohan, Kritika ; Ueda, George ; Kim, Ah Ram ; Jude, Kevin M; Fallas, Jorge A; Guo, Yu ; Hafer, Maximillian ; Miao, Yi ; Saxton, Robert A; Piehler, Jacob ; Sankaran, Vijay G; Baker, David ; Garcia, Christopher K

Topological control of cytokine receptor signaling induces differential effects in hematopoiesis Journal Article

Science, 364 (6442), 2019.

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Boyken, Scott E; Benhaim, Mark A; Busch, Florian ; Jia, Mengxuan ; Bick, Matthew J; Choi, Heejun ; Klima, Jason C; Chen, Zibo ; Walkey, Carl ; Mileant, Alexander ; Sahasrabuddhe, Aniruddha ; Wei, Kathy Y; Hodge, Edgar A; Byron, Sarah ; Quijano-Rubio, Alfredo ; Sankaran, Banumathi ; King, Neil P; Lippincott-Schwartz, Jennifer ; Wysocki, Vicki H; Lee, Kelly K; Baker, David

De novo design of tunable, pH-driven conformational changes Journal Article

Science, 364 (6441), pp. 658-664, 2019.

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Dang, Luke T; Miao, Yi ; Ha, Andrew ; Yuki, Kanako ; Park, Keunwan ; Janda, Claudia Y; Jude, Kevin M; Mohan, Kritika ; Ha, Nhi ; Vallon, Mario ; Yuan, Jenny ; Vilches-Moure, José G; Kuo, Calvin J; Garcia, Christopher K; Baker, David

Receptor subtype discrimination using extensive shape complementary designed interfaces Journal Article

Nature Structural & Molecular Biology, 2019, ISSN: 1545-9985.

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Chen, Zibo ; Johnson, Matthew C; Chen, Jiajun ; Bick, Matthew J; Boyken, Scott E; Lin, Baihan ; De Yoreo, James J; Kollman, Justin M; Baker, David ; DiMaio, Frank

Self-Assembling 2D Arrays with de Novo Protein Building Blocks Journal Article

Journal of the American Chemical Society, 2019.

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de van der Jessica Marcandalli Brooke Fiala, Sebastian Ols Michela Perotti Willem Schueren Joost Snijder Edgar Hodge Mark Benhaim Rashmi Ravichandran Lauren Carter Will Sheffler Livia Brunner Maria Lawrenz Patrice Dubois Antonio Lanzavecchia Federica Sallusto Kelly Lee David Veesler Colin Correnti Lance Stewart David Baker Karin Loré Laurent Perez Neil King K E J P

Induction of Potent Neutralizing Antibody Responses by a Designed Protein Nanoparticle Vaccine for Respiratory Syncytial Virus Journal Article

Cell, 176 (6), pp. 1420-1431, 2019.

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Baker, David

What has de novo protein design taught us about protein folding and biophysics? Journal Article

Protein Science, 28 (4), pp. 678-683, 2019.

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Silva, Daniel-Adriano ; Yu, Shawn ; Ulge, Umut Y; Spangler, Jamie B; Jude, Kevin M; Labão-Almeida, Carlos ; Ali, Lestat R; Quijano-Rubio, Alfredo ; Ruterbusch, Mikel ; Leung, Isabel ; Biary, Tamara ; Crowley, Stephanie J; Marcos, Enrique ; Walkey, Carl D; Weitzner, Brian D; Pardo-Avila, Fátima ; Castellanos, Javier ; Carter, Lauren ; Stewart, Lance ; Riddell, Stanley R; Pepper, Marion ; Bernardes, Gonçalo J L; Dougan, Michael ; Garcia, Christopher K; Baker, David

De novo design of potent and selective mimics of IL-2 and IL-15 Journal Article

Nature, 2019, ISSN: 1476-4687.

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2018

Chen, Zibo ; Boyken, Scott E; Jia, Mengxuan ; Busch, Florian ; Flores-Solis, David ; Bick, Matthew J; Lu, Peilong ; VanAernum, Zachary L; Sahasrabuddhe, Aniruddha ; Langan, Robert A; Bermeo, Sherry ; Brunette, T J; Mulligan, Vikram Khipple ; Carter, Lauren P; DiMaio, Frank ; Sgourakis, Nikolaos G; Wysocki, Vicki H; Baker, David

Programmable design of orthogonal protein heterodimers Journal Article

Nature, 2018, ISSN: 1476-4687.

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Day, Austin L; Greisen, Per ; Doyle, Lindsey ; Schena, Alberto ; Stella, Nephi ; Johnsson, Kai ; Baker, David ; Stoddard, Barry

Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold Journal Article

Protein Engineering, Design and Selection, 2018.

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Romero Romero, Maria Luisa ; Yang, Fan ; Lin, Yu-Ru ; Toth-Petroczy, Agnes ; Berezovsky, Igor N; Goncearenco, Alexander ; Yang, Wen ; Wellner, Alon ; Kumar-Deshmukh, Fanindra ; Sharon, Michal ; Baker, David ; Varani, Gabriele ; Tawfik, Dan S

Simple yet functional phosphate-loop proteins Journal Article

PNAS, 115 (51), pp. E11943–E11950, 2018, ISSN: 0027-8424.

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Shen, Hao ; Fallas, Jorge A; Lynch, Eric ; Sheffler, William ; Parry, Bradley ; Jannetty, Nicholas ; Decarreau, Justin ; Wagenbach, Michael ; Vicente, Juan Jesus ; Chen, Jiajun ; Wang, Lei ; Dowling, Quinton ; Oberdorfer, Gustav ; Stewart, Lance ; Wordeman, Linda ; De Yoreo, James ; Jacobs-Wagner, Christine ; Kollman, Justin ; Baker, David

De novo design of self-assembling helical protein filaments Journal Article

Science, 362 (6415), pp. 705–709, 2018, ISSN: 0036-8075.

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Marcos, Enrique ; Chidyausiku, Tamuka M; McShan, Andrew C; Evangelidis, Thomas ; Nerli, Santrupti ; Carter, Lauren ; Nivón, Lucas G; Davis, Audrey ; Oberdorfer, Gustav ; Tripsianes, Konstantinos ; Sgourakis, Nikolaos G; Baker, David

De novo design of a non-local β-sheet protein with high stability and accuracy Journal Article

Nature Structural & Molecular Biology, 2018, ISSN: 1545-9985.

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Dou*, Jiayi; Vorobieva*, Anastassia A; Sheffler, William; Doyle, Lindsey A; Park, Hahnbeom; Bick, Matthew J; Mao, Binchen; Foight, Glenna W; Lee, Min Yen; Gagnon, Lauren A; Carter, Lauren; Sankaran, Banumathi; Ovchinnikov, Sergey; Marcos, Enrique; Huang, Po-Ssu; Vaughan, Joshua C; Stoddard, Barry L; Baker, David

De novo design of a fluorescence-activating β-barrel Journal Article

Nature, 2018, ISSN: 1476-4687.

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Geiger-Schuller, Kathryn ; Sforza, Kevin ; Yuhas, Max ; Parmeggiani, Fabio ; Baker, David ; Barrick, Doug

Extreme stability in de novo-designed repeat arrays is determined by unusually stable short-range interactions Journal Article

PNAS, 115 (29), pp. 7539-7544, 2018, ISSN: 0027-8424.

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Yue-Ting K. Lau, ; Vladimir Baytshtok, ; Tessa A. Howard, ; Brooke M. Fiala, ; JayLee M. Johnson, ; Lauren P. Carter, ; David Baker, ; Christopher D. Lima, ; Bahl, Christopher D

Discovery and engineering of enhanced SUMO protease enzymes Journal Article

The Journal of Biological Chemistry, 293 , pp. 13224-13233, 2018.

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Park, Hahnbeom ; Ovchinnikov, Sergey ; Kim, David E; DiMaio, Frank ; Baker, David

Protein homology model refinement by large-scale energy optimization Journal Article

Proceedings of the National Academy of Sciences, 115 (12), pp. 3054–3059, 2018, ISSN: 0027-8424.

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Lu, Peilong ; Min, Duyoung ; DiMaio, Frank ; Wei, Kathy Y; Vahey, Michael D; Boyken, Scott E; Chen, Zibo ; Fallas, Jorge A; Ueda, George ; Sheffler, William ; Mulligan, Vikram Khipple ; Xu, Wenqing ; Bowie, James U; Baker, David

Accurate computational design of multipass transmembrane proteins Journal Article

Science, 359 (6379), pp. 1042–1046, 2018, ISSN: 0036-8075.

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Silva, Daniel-Adriano ; Stewart, Lance ; Lam, Kwok-Ho ; Jin, Rongsheng ; Baker, David

Structures and disulfide cross‐linking of de novo designed therapeutic mini‐proteins Journal Article

FEBS Journal, 285 (10), pp. 1783-1785, 2018.

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2017

Hosseinzadeh, Parisa* ; Bhardwaj, Gaurav* ; Mulligan, Vikram Khipple* ; Shortridge, Matthew D; Craven, Timothy W; Pardo-Avila, F{'a}tima ; Rettie, Stephen A; Kim, David E; Silva, Daniel-Adriano ; Ibrahim, Yehia M; Webb, Ian K; Cort, John R; Adkins, Joshua N; Varani, Gabriele ; Baker, David

Comprehensive computational design of ordered peptide macrocycles Journal Article

Science, 358 (6369), pp. 1461-1466, 2017, ISSN: 0036-8075.

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Butterfield, Gabriel L *; Lajoie, Marc J *; Gustafson, Heather H; Sellers, Drew L; Nattermann, Una ; Ellis, Daniel ; Bale, Jacob B; Ke, Sharon ; Lenz, Garreck H; Yehdego, Angelica ; Ravichandran, Rashmi ; Pun, Suzie H; King, Neil P; Baker, David

Evolution of a designed protein assembly encapsulating its own RNA genome Journal Article

Nature, 2017, ISSN: 1476-4687.

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Dou, Jiayi; Doyle, Lindsey; Greisen, Per; Schena, Alberto; Park, Hahnbeom; Johnsson, Kai; Stoddard, Barry; Baker, David

Sampling and energy evaluation challenges in ligand binding protein design Journal Article

Protein Science, 26 , pp. 2426-2437, 2017, ISSN: 1469-896.

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Chevalier*, Aaron; Silva*, Daniel-Adriano; Rocklin*, Gabriel J; Hicks, Derrick R; Vergara, Renan; Murapa, Patience; Bernard, Steffen M; Zhang, Lu; Lam, Kwok-Ho; Yao, Guorui; Bahl, Christopher D; Miyashita, Shin-Ichiro; Goreshnik, Inna; Fuller, James T; Koday, Merika T; Jenkins, Cody M; Colvin, Tom; Carter, Lauren; Bohn, Alan; Bryan, Cassie M; Fernández-Velasco, Alejandro D; Stewart, Lance; Dong, Min; Huang, Xuhui; Jin, Rongsheng; Wilson, Ian A; Fuller, Deborah H; Baker, David

Massively parallel de novo protein design for targeted therapeutics Journal Article

Nature, 550 (7674), pp. 74-79, 2017, ISSN: 0028-0836.

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Sergey Ovchinnikov Hahnbeom Park, David Kim Frank DiMaio David Baker E

Protein structure prediction using Rosetta in CASP12 Journal Article

Proteins, 2017.

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Bick, Matthew J*; Greisen, Per J*; Morey, Kevin J; Antunes, Mauricio S; La, David ; Sankaran, Banumathi ; Reymond, Luc ; Johnsson, Kai ; Medford, June I; Baker, David

Computational design of environmental sensors for the potent opioid fentanyl Journal Article

eLife Sciences Publications, 6 , pp. e28909, 2017, ISBN: 2050-084X.

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

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.

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Lin, Yu-Ru; Koga, Nobuyasu; Vorobiev, Sergey M; Baker, David

Cyclic oligomer design with de novo αβ-proteins Journal Article

Protein Science, 2017.

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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.

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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.

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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, Stephanie; Procko, Erik; Margineantu, Daciana; Lee, Erinna F; Shen, Betty W; Zelter, Alex; Silva, Daniel-Adriano; and Chawla, Kusum; Herold, Marco J; Garnier, Jean-Marc; Johnson, Richard; MacCoss, Michael J; Lessene, Guillaume; Davis, Trisha N; Stayton, Patrick S; Stoddard, Barry L; Fairlie, Douglas W; Hockenbery, David M; Baker, David

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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461 entries « 1 of 10 »