Publications

Preprints are available on bioRxiv.

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21 entries « 1 of 2 »
1.

Agarwal, Dilip Kumar; Hunt, Andrew C.; Shekhawat, Gajendra S.; Carter, Lauren; Chan, Sidney; Wu, Kejia; Cao, Longxing; Baker, David; Lorenzo-Redondo, Ramon; Ozer, Egon A.; Simons, Lacy M.; Hultquist, Judd F.; Jewett, Michael C.; Dravid, Vinayak P.

Rapid and Sensitive Detection of Antigen from SARS-CoV-2 Variants of Concern by a Multivalent Minibinder-Functionalized Nanomechanical Sensor Bachelor Thesis

2022.

Abstract | Links | BibTeX

2.

Hunt, Andrew C.; Case, James Brett; Park, Young-Jun; Cao, Longxing; Wu, Kejia; Walls, Alexandra C.; Liu, Zhuoming; Bowen, John E.; Yeh, Hsien-Wei; Saini, Shally; Helms, Louisa; Zhao, Yan Ting; Hsiang, Tien-Ying; Starr, Tyler N.; Goreshnik, Inna; Kozodoy, Lisa; Carter, Lauren; Ravichandran, Rashmi; Green, Lydia B.; Matochko, Wadim L.; Thomson, Christy A.; Vögeli, Bastian; Krüger, Antje; VanBlargan, Laura A.; Chen, Rita E.; Ying, Baoling; Bailey, Adam L.; Kafai, Natasha M.; Boyken, Scott E.; Ljubetič, Ajasja; Edman, Natasha; Ueda, George; Chow, Cameron M.; Johnson, Max; Addetia, Amin; Navarro, Mary Jane; Panpradist, Nuttada; Gale, Michael; Freedman, Benjamin S.; Bloom, Jesse D.; Ruohola-Baker, Hannele; Whelan, Sean P. J.; Stewart, Lance; Diamond, Michael S.; Veesler, David; Jewett, Michael C.; Baker, David

Multivalent designed proteins neutralize SARS-CoV-2 variants of concern and confer protection against infection in mice Journal Article

In: Science Translational Medicine, 2022.

Abstract | Links | BibTeX

3.

Cao, Longxing; Coventry, Brian; Goreshnik, Inna; Huang, Buwei; Park, Joon Sung; Jude, Kevin M.; Marković, Iva; Kadam, Rameshwar U.; Verschueren, Koen H. G.; Verstraete, Kenneth; Walsh, Scott Thomas Russell; Bennett, Nathaniel; Phal, Ashish; Yang, Aerin; Kozodoy, Lisa; DeWitt, Michelle; Picton, Lora; Miller, Lauren; Strauch, Eva-Maria; DeBouver, Nicholas D.; Pires, Allison; Bera, Asim K.; Halabiya, Samer; Hammerson, Bradley; Yang, Wei; Bernard, Steffen; Stewart, Lance; Wilson, Ian A.; Ruohola-Baker, Hannele; Schlessinger, Joseph; Lee, Sangwon; Savvides, Savvas N.; Garcia, K. Christopher; Baker, David

Design of protein binding proteins from target structure alone Journal Article

In: Nature, 2022.

Abstract | Links | BibTeX

4.

Levy, Shiri; Somasundaram, Logeshwaran; Raj, Infencia Xavier; Ic-Mex, Diego; Phal, Ashish; Schmidt, Sven; Ng, Weng I.; Mar, Daniel; Decarreau, Justin; Moss, Nicholas; Alghadeer, Ammar; Honkanen, Henrik; Sarthy, Jay; Vitanza, Nicholas; Hawkins, R. David; Mathieu, Julie; Wang, Yuliang; Baker, David; Bomsztyk, Karol; Ruohola-Baker, Hannele

dCas9 fusion to computer-designed PRC2 inhibitor reveals functional TATA box in distal promoter region Journal Article

In: Cell Reports, 2022.

Abstract | Links | BibTeX

5.

Bryan, Cassie M.; Rocklin, Gabriel J.; Bick, Matthew J.; Ford, Alex; Majri-Morrison, Sonia; Kroll, Ashley V.; Miller, Chad J.; Carter, Lauren; Goreshnik, Inna; Kang, Alex; DiMaio, Frank; Tarbell, Kristin V.; Baker, David

Computational design of a synthetic PD-1 agonist Journal Article

In: Proceedings of the National Academy of Sciences, vol. 118, no. 29, 2021.

Abstract | Links | BibTeX

6.

Hosseinzadeh, Parisa; Watson, Paris R.; Craven, Timothy W.; Li, Xinting; Rettie, Stephen; Pardo-Avila, Fátima; Bera, Asim K.; Mulligan, Vikram Khipple; Lu, Peilong; Ford, Alexander S.; Weitzner, Brian D.; Stewart, Lance J.; Moyer, Adam P.; Di Piazza, Maddalena; Whalen, Joshua G.; Greisen, Per Jr.; Christianson, David W.; Baker, David

Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites Journal Article

In: Nature Communications, 2021.

Abstract | Links | BibTeX

7.

Sahtoe, Danny D.; Coscia, Adrian; Mustafaoglu, Nur; Miller, Lauren M.; Olal, Daniel; Vulovic, Ivan; Yu, Ta-Yi; Goreshnik, Inna; Lin, Yu-Ru; Clark, Lars; Busch, Florian; Stewart, Lance; Wysocki, Vicki H.; Ingber, Donald E.; Abraham, Jonathan; Baker, David

Transferrin receptor targeting by de novo sheet extension Journal Article

In: Proceedings of the National Academy of Sciences, 2021.

Abstract | Links | BibTeX

8.

Quijano-Rubio, Alfredo; Yeh, Hsien-Wei; Park, Jooyoung; Lee, Hansol; Langan, Robert A.; Boyken, Scott E.; Lajoie, Marc J.; Cao, Longxing; Chow, Cameron M.; Miranda, Marcos C.; Wi, Jimin; Hong, Hyo Jeong; Stewart, Lance; Oh, Byung-Ha; Baker, David

De novo design of modular and tunable protein biosensors Journal Article

In: Nature, 2021.

Abstract | Links | BibTeX

9.

Cao, Longxing; Goreshnik, Inna; Coventry, Brian; Case, James Brett; Miller, Lauren; Kozodoy, Lisa; Chen, Rita E.; Carter, Lauren; Walls, Alexandra C.; Park, Young-Jun; Strauch, Eva-Maria; Stewart, Lance; Diamond, Michael S.; Veesler, David; Baker, David

De novo design of picomolar SARS-CoV-2 miniprotein inhibitors Journal Article

In: Science, 2020.

Abstract | Links | BibTeX

10.

Basanta, Benjamin; Bick, Matthew J.; Bera, Asim K.; Norn, Christoffer; Chow, Cameron M.; Carter, Lauren P.; Goreshnik, Inna; Dimaio, Frank; Baker, David

An enumerative algorithm for de novo design of proteins with diverse pocket structures Journal Article

In: Proceedings of the National Academy of Sciences, vol. 117, no. 36, pp. 22135–22145, 2020, ISBN: 0027-8424.

Abstract | Links | BibTeX

11.

Brunette, TJ; Bick, Matthew J.; Hansen, Jesse M.; Chow, Cameron M.; Kollman, Justin M.; Baker, David

Modular repeat protein sculpting using rigid helical junctions Journal Article

In: Proceedings of the National Academy of Sciences, 2020.

Abstract | Links | BibTeX

12.

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

In: PNAS, vol. 115, no. 51, pp. E11943–E11950, 2018, ISSN: 0027-8424.

Abstract | Links | BibTeX

13.

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

In: FEBS Journal, vol. 285, no. 10, pp. 1783-1785, 2018.

Abstract | Links | BibTeX

14.

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, D. Alejandro; 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

In: Nature, vol. 550, no. 7674, pp. 74-79, 2017, ISSN: 0028-0836.

Abstract | Links | BibTeX

15.

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

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

Abstract | Links | BibTeX

16.

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

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

Abstract | Links | BibTeX

17.

Moretti, Rocco; Fleishman, Sarel J; Agius, Rudi; Torchala, Mieczyslaw; Bates, Paul A; Kastritis, Panagiotis L; ao P G L M Rodrigues, Jo; 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

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

Abstract | Links | BibTeX

18.

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

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

Abstract | Links | BibTeX

19.

Whitehead, Timothy A; Baker, David; Fleishman, Sarel J

Computational design of novel protein binders and experimental affinity maturation Journal Article

In: Methods in enzymology, vol. 523, pp. 1-19, 2013, ISSN: 1557-7988.

Abstract | Links | BibTeX

20.

Fleishman, Sarel J; Corn, Jacob E; Strauch, Eva-Maria; Whitehead, Timothy A; Karanicolas, John; Baker, David

Hotspot-centric de novo design of protein binders Journal Article

In: Journal of molecular biology, vol. 413, pp. 1047-62, 2011, ISSN: 1089-8638.

Abstract | Links | BibTeX

21 entries « 1 of 2 »

 

2022

FROM THE LAB

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Andrew C. Hunt, James Brett Case, Young-Jun Park, Longxing Cao, Kejia Wu, Alexandra C. Walls, Zhuoming Liu, John E. Bowen, Hsien-Wei Yeh, Shally Saini, Louisa Helms, Yan Ting Zhao, Tien-Ying Hsiang, Tyler N. Starr, Inna Goreshnik, Lisa Kozodoy, Lauren Carter, Rashmi Ravichandran, Lydia B. Green, Wadim L. Matochko, Christy A. Thomson, Bastian Vögeli, Antje Krüger, Laura A. VanBlargan, Rita E. Chen, Baoling Ying, Adam L. Bailey, Natasha M. Kafai, Scott E. Boyken, Ajasja Ljubetič, Natasha Edman, George Ueda, Cameron M. Chow, Max Johnson, Amin Addetia, Mary Jane Navarro, Nuttada Panpradist, Michael Gale, Benjamin S. Freedman, Jesse D. Bloom, Hannele Ruohola-Baker, Sean P. J. Whelan, Lance Stewart, Michael S. Diamond, David Veesler, Michael C. Jewett, David Baker

Multivalent designed proteins neutralize SARS-CoV-2 variants of concern and confer protection against infection in mice Journal Article

In: Science Translational Medicine, 2022.

Abstract | Links

Cao, Longxing, Coventry, Brian, Goreshnik, Inna, Huang, Buwei, Park, Joon Sung, Jude, Kevin M., Marković, Iva, Kadam, Rameshwar U., Verschueren, Koen H. G., Verstraete, Kenneth, Walsh, Scott Thomas Russell, Bennett, Nathaniel, Phal, Ashish, Yang, Aerin, Kozodoy, Lisa, DeWitt, Michelle, Picton, Lora, Miller, Lauren, Strauch, Eva-Maria, DeBouver, Nicholas D., Pires, Allison, Bera, Asim K., Halabiya, Samer, Hammerson, Bradley, Yang, Wei, Bernard, Steffen, Stewart, Lance, Wilson, Ian A., Ruohola-Baker, Hannele, Schlessinger, Joseph, Lee, Sangwon, Savvides, Savvas N., Garcia, K. Christopher, Baker, David

Design of protein binding proteins from target structure alone Journal Article

In: Nature, 2022.

Abstract | Links

COLLABORATOR LED

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Agarwal, Dilip Kumar and Hunt, Andrew C. and Shekhawat, Gajendra S. and Carter, Lauren and Chan, Sidney and Wu, Kejia and Cao, Longxing and Baker, David and Lorenzo-Redondo, Ramon and Ozer, Egon A. and Simons, Lacy M. and Hultquist, Judd F. and Jewett, Michael C. and Dravid, Vinayak P.

Rapid and Sensitive Detection of Antigen from SARS-CoV-2 Variants of Concern by a Multivalent Minibinder-Functionalized Nanomechanical Sensor Bachelor Thesis

2022.

Abstract | Links

Shiri Levy, Logeshwaran Somasundaram, Infencia Xavier Raj, Diego Ic-Mex, Ashish Phal, Sven Schmidt, Weng I. Ng, Daniel Mar, Justin Decarreau, Nicholas Moss, Ammar Alghadeer, Henrik Honkanen, Jay Sarthy, Nicholas Vitanza, R. David Hawkins, Julie Mathieu, Yuliang Wang, David Baker, Karol Bomsztyk, Hannele Ruohola-Baker

dCas9 fusion to computer-designed PRC2 inhibitor reveals functional TATA box in distal promoter region Journal Article

In: Cell Reports, 2022.

Abstract | Links

2021

FROM THE LAB

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Bryan, Cassie M. and Rocklin, Gabriel J. and Bick, Matthew J. and Ford, Alex and Majri-Morrison, Sonia and Kroll, Ashley V. and Miller, Chad J. and Carter, Lauren and Goreshnik, Inna and Kang, Alex and DiMaio, Frank and Tarbell, Kristin V. and Baker, David

Computational design of a synthetic PD-1 agonist Journal Article

In: Proceedings of the National Academy of Sciences, vol. 118, no. 29, 2021.

Abstract | Links

Hosseinzadeh, Parisa and Watson, Paris R. and Craven, Timothy W. and Li, Xinting and Rettie, Stephen and Pardo-Avila, Fátima and Bera, Asim K. and Mulligan, Vikram Khipple and Lu, Peilong and Ford, Alexander S. and Weitzner, Brian D. and Stewart, Lance J. and Moyer, Adam P. and Di Piazza, Maddalena and Whalen, Joshua G. and Greisen, Per Jr. and Christianson, David W. and Baker, David

Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites Journal Article

In: Nature Communications, 2021.

Abstract | Links

Sahtoe, Danny D., Coscia, Adrian, Mustafaoglu, Nur, Miller, Lauren M., Olal, Daniel, Vulovic, Ivan, Yu, Ta-Yi, Goreshnik, Inna, Lin, Yu-Ru, Clark, Lars, Busch, Florian, Stewart, Lance, Wysocki, Vicki H., Ingber, Donald E., Abraham, Jonathan, Baker, David

Transferrin receptor targeting by de novo sheet extension Journal Article

In: Proceedings of the National Academy of Sciences, 2021.

Abstract | Links

Quijano-Rubio, Alfredo and Yeh, Hsien-Wei and Park, Jooyoung and Lee, Hansol and Langan, Robert A. and Boyken, Scott E. and Lajoie, Marc J. and Cao, Longxing and Chow, Cameron M. and Miranda, Marcos C. and Wi, Jimin and Hong, Hyo Jeong and Stewart, Lance and Oh, Byung-Ha and Baker, David

De novo design of modular and tunable protein biosensors Journal Article

In: Nature, 2021.

Abstract | Links

COLLABORATOR LED

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Sorry, no publications matched your criteria.

2020

FROM THE LAB

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Cao, Longxing, Goreshnik, Inna, Coventry, Brian, Case, James Brett, Miller, Lauren, Kozodoy, Lisa, Chen, Rita E., Carter, Lauren, Walls, Alexandra C., Park, Young-Jun, Strauch, Eva-Maria, Stewart, Lance, Diamond, Michael S., Veesler, David, Baker, David

De novo design of picomolar SARS-CoV-2 miniprotein inhibitors Journal Article

In: Science, 2020.

Abstract | Links

Basanta, Benjamin, Bick, Matthew J., Bera, Asim K., Norn, Christoffer, Chow, Cameron M., Carter, Lauren P., Goreshnik, Inna, Dimaio, Frank, Baker, David

An enumerative algorithm for de novo design of proteins with diverse pocket structures Journal Article

In: Proceedings of the National Academy of Sciences, vol. 117, no. 36, pp. 22135–22145, 2020, ISBN: 0027-8424.

Abstract | Links

Brunette, TJ, Bick, Matthew J., Hansen, Jesse M., Chow, Cameron M., Kollman, Justin M., Baker, David

Modular repeat protein sculpting using rigid helical junctions Journal Article

In: Proceedings of the National Academy of Sciences, 2020.

Abstract | Links

COLLABORATOR LED

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Sorry, no publications matched your criteria.

2019

FROM THE LAB

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2018

FROM THE LAB

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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

In: FEBS Journal, vol. 285, no. 10, pp. 1783-1785, 2018.

Abstract | Links

COLLABORATOR LED

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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

In: PNAS, vol. 115, no. 51, pp. E11943–E11950, 2018, ISSN: 0027-8424.

Abstract | Links

2017–1998

ALL PAPERS

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2017

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

Massively parallel de novo protein design for targeted therapeutics Journal Article

In: Nature, vol. 550, no. 7674, pp. 74-79, 2017, ISSN: 0028-0836.

Abstract | Links

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

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

Abstract | Links

2015

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

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

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

Abstract | Links

2013

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

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

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

Abstract | Links

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

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

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

Abstract | Links

Timothy A Whitehead, David Baker, Sarel J Fleishman

Computational design of novel protein binders and experimental affinity maturation Journal Article

In: Methods in enzymology, vol. 523, pp. 1-19, 2013, ISSN: 1557-7988.

Abstract | Links

2011

Sarel J Fleishman, Timothy A Whitehead, Eva-Maria Strauch, Jacob E Corn, Sanbo Qin, Huan-Xiang Zhou, Julie C Mitchell, Omar N A Demerdash, Mayuko Takeda-Shitaka, Genki Terashi, Iain H Moal, Xiaofan Li, Paul A Bates, Martin Zacharias, Hahnbeom Park, Jun-su Ko, Hasup Lee, Chaok Seok, Thomas Bourquard, Julie Bernauer, Anne Poupon, J'er^ome Az'e, Seren Soner, Sefik Kerem Ovali, Pemra Ozbek, Nir Ben Tal, T"urkan Haliloglu, Howook Hwang, Thom Vreven, Brian G Pierce, Zhiping Weng, Laura P'erez-Cano, Carles Pons, Juan Fern'andez-Recio, Fan Jiang, Feng Yang, Xinqi Gong, Libin Cao, Xianjin Xu, Bin Liu, Panwen Wang, Chunhua Li, Cunxin Wang, Charles H Robert, Mainak Guharoy, Shiyong Liu, Yangyu Huang, Lin Li, Dachuan Guo, Ying Chen, Yi Xiao, Nir London, Zohar Itzhaki, Ora Schueler-Furman, Yuval Inbar, Vladimir Potapov, Mati Cohen, Gideon Schreiber, Yuko Tsuchiya, Eiji Kanamori, Daron M Standley, Haruki Nakamura, Kengo Kinoshita, Camden M Driggers, Robert G Hall, Jessica L Morgan, Victor L Hsu, Jian Zhan, Yuedong Yang, Yaoqi Zhou, Panagiotis L Kastritis, Alexandre M J J Bonvin, Weiyi Zhang, Carlos J Camacho, Krishna P Kilambi, Aroop Sircar, Jeffrey J Gray, Masahito Ohue, Nobuyuki Uchikoga, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama, Raed Khashan, Stephen Bush, Denis Fouches, Alexander Tropsha, Juan Esquivel-Rodr'iguez, Daisuke Kihara, P Benjamin Stranges, Ron Jacak, Brian Kuhlman, Sheng-You Huang, Xiaoqin Zou, Shoshana J Wodak, Joel Janin, David Baker

Community-wide assessment of protein-interface modeling suggests improvements to design methodology Journal Article

In: Journal of Molecular Biology, vol. 414, pp. 289-302, 2011, ISSN: 1089-8638.

Abstract | Links

Sarel J Fleishman, Jacob E Corn, Eva-Maria Strauch, Timothy A Whitehead, John Karanicolas, David Baker

Hotspot-centric de novo design of protein binders Journal Article

In: Journal of molecular biology, vol. 413, pp. 1047-62, 2011, ISSN: 1089-8638.

Abstract | Links