Publications

Preprints are available on bioRxiv.

 

2022

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2021

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2020

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2019

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2018

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2017–1998

ALL PAPERS
437 entries « 2 of 15 »

2015

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

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

In: Nature Methods, 2015.

Abstract | Links

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

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

In: Proteins, 2015.

Abstract | Links

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

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

In: Elife, 2015.

Abstract | Links

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

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

In: Archives of Toxicology, 2015.

Abstract | Links

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

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

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

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

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

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

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

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

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

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

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

In: eLife, 2015.

Abstract | Links

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

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

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

Abstract | Links

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

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

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

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

Shane Gonen, Frank DiMaio, Tamir Gonen, David Baker

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

Abstract | Links

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

Hahnbeom Park, Frank DiMaio, David Baker

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

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

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

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

Abstract | Links

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

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

In: Nature methods, 2015, ISSN: 1548-7105.

Abstract | Links

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

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

In: Nature methods, 2015, ISSN: 1548-7105.

Abstract | Links

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

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

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

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

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

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

Abstract | Links

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

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

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

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

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

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

Abstract | Links

Intrinsic disorder drives N-terminal ubiquitination by Ube2w Journal Article

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

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

Abstract | Links

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

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

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

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

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

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

Abstract | Links

2014

Massively parallel determination and modeling of endonuclease substrate specificity Journal Article

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

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

Abstract | Links

A General Computational Approach for Repeat Protein Design. Journal Article

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

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

Abstract | Links

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

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

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

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High thermodynamic stability of parametrically designed helical bundles Journal Article

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

In: Science, vol. 346, pp. 481-85, 2014.

Abstract | Links

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

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

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

Abstract | Links

WeFold: a coopetition for protein structure prediction. Journal Article

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

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

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

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

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

Abstract | Links

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

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

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

Abstract | Links

437 entries « 2 of 15 »