Publications

Preprints are available on bioRxiv.

Show all

63 entries « 1 of 4 »
1.

Bhardwaj, Gaurav; O’Connor, Jacob; Rettie, Stephen; Huang, Yen-Hua; Ramelot, Theresa A.; Mulligan, Vikram Khipple; Alpkilic, Gizem Gokce; Palmer, Jonathan; Bera, Asim K.; Bick, Matthew J.; Piazza, Maddalena Di; Li, Xinting; Hosseinzadeh, Parisa; Craven, Timothy W.; Tejero, Roberto; Lauko, Anna; Choi, Ryan; Glynn, Calina; Dong, Linlin; Griffin, Robert; van Voorhis, Wesley C.; Rodriguez, Jose; Stewart, Lance; Montelione, Gaetano T.; Craik, David; Baker, David

Accurate de novo design of membrane-traversing macrocycles Bachelor Thesis

2022.

Abstract | Links | BibTeX

2.

Macé, Kévin; Vadakkepat, Abhinav K.; Redzej, Adam; Lukoyanova, Natalya; Oomen, Clasien; Braun, Nathalie; Ukleja, Marta; Lu, Fang; Costa, Tiago R. D.; Orlova, Elena V.; Baker, David; Cong, Qian; Waksman, Gabriel

Cryo-EM structure of a type IV secretion system Bachelor Thesis

2022.

Abstract | Links | BibTeX

3.

Levine, Paul M.; Craven, Timothy W.; Li, Xinting; Balana, Aaron T.; Bird, Gregory H.; Godes, Marina; Salveson, Patrick J.; Erickson, Patrick W.; Lamb, Mila; Ahlrichs, Maggie; Murphy, Michael; Ogohara, Cassandra; Said, Meerit Y.; Walensky, Loren D.; Pratt, Matthew R.; Baker, David

Generation of Potent and Stable GLP-1 Analogues Via “Serine Ligation” Journal Article

In: ACS Chemical Biology, 2022.

Abstract | Links | BibTeX

4.

Yao, Sicong; Moyer, Adam; Zheng, Yiwu; Shen, Yang; Meng, Xiaoting; Yuan, Chong; Zhao, Yibing; Yao, Hongwei; Baker, David; Wu, Chuanliu

De novo design and directed folding of disulfide-bridged peptide heterodimers Journal Article

In: Nature Communications, 2022.

Abstract | Links | BibTeX

5.

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

6.

Mulligan, Vikram Khipple; Workman, Sean; Sun, Tianjun; Rettie, Stephen; Li, Xinting; Worrall, Liam J.; Craven, Timothy W.; King, Dustin T.; Hosseinzadeh, Parisa; Watkins, Andrew M.; Renfrew, P. Douglas; Guffy, Sharon; Labonte, Jason W.; Moretti, Rocco; Bonneau, Richard; Strynadka, Natalie C. J.; Baker, David

Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1 Journal Article

In: Proceedings of the National Academy of Sciences, vol. 118, no. 12, 2021.

Abstract | Links | BibTeX

7.

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

8.

Mulligan, Vikram Khipple; Kang, Christine S.; Sawaya, Michael R.; Rettie, Stephen; Li, Xinting; Antselovich, Inna; Craven, Timothy W.; Watkins, Andrew M.; Labonte, Jason W.; DiMaio, Frank; Yeates, Todd O.; Baker, David

Computational design of mixed chirality peptide macrocycles with internal symmetry Journal Article

In: Protein Science, 2020.

Abstract | Links | BibTeX

9.

Xu, Chunfu; Lu, Peilong; El-Din, Tamer M. Gamal; Pei, Xue Y.; Johnson, Matthew C.; Uyeda, Atsuko; Bick, Matthew J.; Xu, Qi; Jiang, Daohua; Bai, Hua; Reggiano, Gabriella; Hsia, Yang; Brunette, T J; Dou, Jiayi; Ma, Dan; Lynch, Eric M.; Boyken, Scott E.; Huang, Po-Ssu; Stewart, Lance; DiMaio, Frank; Kollman, Justin M.; Luisi, Ben F.; Matsuura, Tomoaki; Catterall, William A.; Baker, David

Computational design of transmembrane pores Journal Article

In: Nature, vol. 585, pp. 129–134, 2020.

Abstract | Links | BibTeX

10.

Kirkpatrick, Robin L.; Lewis, Kieran; Langan, Robert A.; Lajoie, Marc J.; Boyken, Scott E.; Eakman, Madeleine; Baker, David; Zalatan, Jesse G.

Conditional Recruitment to a DNA-Bound CRISPR–Cas Complex Using a Colocalization-Dependent Protein Switch Journal Article

In: ACS Synthetic Biology, 2020.

Abstract | Links | BibTeX

11.

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

In: Nature, 2019.

Abstract | Links | BibTeX

12.

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

In: Nature, 2019.

Abstract | Links | BibTeX

13.

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

In: Science, vol. 362, no. 6415, pp. 705–709, 2018, ISSN: 0036-8075.

Abstract | Links | BibTeX

14.

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

In: PNAS, vol. 115, no. 29, pp. 7539-7544, 2018, ISSN: 0027-8424.

Abstract | Links | BibTeX

15.

Hosseinzadeh, Parisa*; Bhardwaj, Gaurav*; Mulligan, Vikram Khipple*; Shortridge, Matthew D.; Craven, Timothy W.; Pardo-Avila, F'atima; 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

In: Science, vol. 358, no. 6369, pp. 1461-1466, 2017, ISSN: 0036-8075.

Abstract | Links | BibTeX

16.

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

In: Nature, 2017, ISSN: 1476-4687.

Abstract | Links | BibTeX

17.

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 P. Carter; 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

In: Nature, 2016.

Abstract | Links | BibTeX

18.

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

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

Abstract | Links | BibTeX

19.

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

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

Abstract | Links | BibTeX

20.

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

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

Abstract | Links | BibTeX

63 entries « 1 of 4 »

 

2022

FROM THE LAB

Show all

Gaurav Bhardwaj, Jacob O’Connor, Stephen Rettie, Yen-Hua Huang, Theresa A. Ramelot, Vikram Khipple Mulligan, Gizem Gokce Alpkilic, Jonathan Palmer, Asim K. Bera, Matthew J. Bick, Maddalena Di Piazza, Xinting Li, Parisa Hosseinzadeh, Timothy W. Craven, Roberto Tejero, Anna Lauko, Ryan Choi, Calina Glynn, Linlin Dong, Robert Griffin, Wesley C. van Voorhis, Jose Rodriguez, Lance Stewart, Gaetano T. Montelione, David Craik, David Baker

Accurate de novo design of membrane-traversing macrocycles Bachelor Thesis

2022.

Abstract | Links

Levine, Paul M., Craven, Timothy W., Li, Xinting, Balana, Aaron T., Bird, Gregory H., Godes, Marina, Salveson, Patrick J., Erickson, Patrick W., Lamb, Mila, Ahlrichs, Maggie, Murphy, Michael, Ogohara, Cassandra, Said, Meerit Y., Walensky, Loren D., Pratt, Matthew R., Baker, David

Generation of Potent and Stable GLP-1 Analogues Via “Serine Ligation” Journal Article

In: ACS Chemical Biology, 2022.

Abstract | Links

COLLABORATOR LED

Show all

Macé, Kévin and Vadakkepat, Abhinav K. and Redzej, Adam and Lukoyanova, Natalya and Oomen, Clasien and Braun, Nathalie and Ukleja, Marta and Lu, Fang and Costa, Tiago R. D. and Orlova, Elena V. and Baker, David and Cong, Qian and Waksman, Gabriel

Cryo-EM structure of a type IV secretion system Bachelor Thesis

2022.

Abstract | Links

Yao, Sicong, Moyer, Adam, Zheng, Yiwu, Shen, Yang, Meng, Xiaoting, Yuan, Chong, Zhao, Yibing, Yao, Hongwei, Baker, David, Wu, Chuanliu

De novo design and directed folding of disulfide-bridged peptide heterodimers Journal Article

In: Nature Communications, 2022.

Abstract | Links

2021

FROM THE LAB

Show all

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

Mulligan, Vikram Khipple, Workman, Sean, Sun, Tianjun, Rettie, Stephen, Li, Xinting, Worrall, Liam J., Craven, Timothy W., King, Dustin T., Hosseinzadeh, Parisa, Watkins, Andrew M., Renfrew, P. Douglas, Guffy, Sharon, Labonte, Jason W., Moretti, Rocco, Bonneau, Richard, Strynadka, Natalie C. J., Baker, David

Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1 Journal Article

In: Proceedings of the National Academy of Sciences, vol. 118, no. 12, 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

Show all

Sorry, no publications matched your criteria.

2020

FROM THE LAB

Show all

Vikram Khipple Mulligan, Christine S. Kang, Michael R. Sawaya, Stephen Rettie, Xinting Li, Inna Antselovich, Timothy W. Craven, Andrew M. Watkins, Jason W. Labonte, Frank DiMaio, Todd O. Yeates, David Baker

Computational design of mixed chirality peptide macrocycles with internal symmetry Journal Article

In: Protein Science, 2020.

Abstract | Links

Chunfu Xu, Peilong Lu, Tamer M. Gamal El-Din, Xue Y. Pei, Matthew C. Johnson, Atsuko Uyeda, Matthew J. Bick, Qi Xu, Daohua Jiang, Hua Bai, Gabriella Reggiano, Yang Hsia, T J Brunette, Jiayi Dou, Dan Ma, Eric M. Lynch, Scott E. Boyken, Po-Ssu Huang, Lance Stewart, Frank DiMaio, Justin M. Kollman, Ben F. Luisi, Tomoaki Matsuura, William A. Catterall, David Baker

Computational design of transmembrane pores Journal Article

In: Nature, vol. 585, pp. 129–134, 2020.

Abstract | Links

COLLABORATOR LED

Show all

Robin L. Kirkpatrick, Kieran Lewis, Robert A. Langan, Marc J. Lajoie, Scott E. Boyken, Madeleine Eakman, David Baker, Jesse G. Zalatan

Conditional Recruitment to a DNA-Bound CRISPR–Cas Complex Using a Colocalization-Dependent Protein Switch Journal Article

In: ACS Synthetic Biology, 2020.

Abstract | Links

2019

FROM THE LAB

Show all

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

In: Nature, 2019.

Abstract | Links

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

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

In: Nature, 2019.

Abstract | Links

COLLABORATOR LED

Show all

Sorry, no publications matched your criteria.

2018

FROM THE LAB

Show all

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

In: Science, vol. 362, no. 6415, pp. 705–709, 2018, ISSN: 0036-8075.

Abstract | Links

COLLABORATOR LED

Show all

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

In: PNAS, vol. 115, no. 29, pp. 7539-7544, 2018, ISSN: 0027-8424.

Abstract | Links

2017–1998

ALL PAPERS

Show all

49 entries « 1 of 2 »

2017

Hosseinzadeh, Parisa*, Bhardwaj, Gaurav*, Mulligan, Vikram Khipple*, Shortridge, Matthew D., Craven, Timothy W., Pardo-Avila, F'atima, 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

In: Science, vol. 358, no. 6369, pp. 1461-1466, 2017, ISSN: 0036-8075.

Abstract | Links

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

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

In: Nature, 2017, ISSN: 1476-4687.

Abstract | Links

2016

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

Accurate de novo design of hyperstable constrained peptides Journal Article

In: Nature, 2016.

Abstract | Links

2015

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

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

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

Abstract | Links

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

Exploring the repeat protein universe through computational protein design Journal Article

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

Abstract | Links

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

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

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

Abstract | Links

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

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

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

Abstract | Links

2014

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

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

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

Abstract | Links

Chris King, Esteban N Garza, Ronit Mazor, Jonathan L Linehan, Ira Pastan, Marion Pepper, David Baker

Removing T-cell epitopes with computational protein design. Journal Article

In: Proceedings of the National Academy of Sciences of the United States of America, 2014, ISSN: 1091-6490.

Abstract | Links

Tyler D Shropshire, Jack Reifert, Sridharan Rajagopalan, David Baker, Stuart C Feinstein, Patrick S Daugherty

Amyloid β peptide cleavage by kallikrein 7 attenuates fibril growth and rescues neurons from Aβ-mediated toxicity in vitro. Journal Article

In: Biological chemistry, vol. 395, pp. 109-18, 2014, ISSN: 1437-4315.

Abstract | Links

Pierre Leblanc, Leonard Moise, Cybelle Luza, Kanawat Chantaralawan, Lynchy Lezeau, Jianping Yuan, Mary Field, Daniel Richer, Christine Boyle, William D Martin, Jordan B Fishman, Eric A Berg, David Baker, Brandon Zeigler, Dale E Mais, William Taylor, Russell Coleman, H Shaw Warren, Jeffrey A Gelfand, Anne S De Groot, Timothy Brauns, Mark C Poznansky

VaxCelerate II: rapid development of a self-assembling vaccine for Lassa fever. Journal Article

In: Human vaccines & immunotherapeutics, vol. 10, pp. 3022-38, 2014, ISSN: 2164-554X.

Abstract | Links

2013

MA Molski, JL Goodman, FC Chou, D Baker, R Das, A Schepartz

Remodeling a beta-peptide bundle Journal Article

In: Chemical Science, vol. 4, pp. 319-324, 2013, ISSN: 2041-6520.

Abstract | Links

2012

Sydney R Gordon, Elizabeth J Stanley, Sarah Wolf, Angus Toland, Sean J Wu, Daniel Hadidi, Jeremy H Mills, David Baker, Ingrid Swanson Pultz, Justin B Siegel

Computational Design of an α-gliadin Peptidase Journal Article

In: Journal of the American Chemical Society, vol. 134, pp. 20513-20, 2012, ISSN: 1520-5126.

Abstract | Links

Sarah Baxter, Abigail R Lambert, Ryan Kuhar, Jordan Jarjour, Nadia Kulshina, Fabio Parmeggiani, Patrick Danaher, Jacob Gano, David Baker, Barry L Stoddard, Andrew M Scharenberg

Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases. Journal Article

In: Nucleic acids research, vol. 40, pp. 7985-8000, 2012, ISSN: 1362-4962.

Abstract | Links

Assaf Alon, Iris Grossman, Yair Gat, Vamsi K Kodali, Frank DiMaio, Tevie Mehlman, Gilad Haran, David Baker, Colin Thorpe, Deborah Fass

The dynamic disulphide relay of quiescin sulphydryl oxidase Journal Article

In: Nature, vol. 488, pp. 414-8, 2012, ISSN: 1476-4687.

Abstract | Links

2011

Sean J Wu, Christopher B Eiben, John H Carra, Ivan Huang, David Zong, Peixian Liu, Cindy T Wu, Jeff Nivala, Josef Dunbar, Tomas Huber, Jeffrey Senft, Rowena Schokman, Matthew D Smith, Jeremy H Mills, Arthur M Friedlander, David Baker, Justin B Siegel

Improvement of a potential anthrax therapeutic by computational protein design Journal Article

In: The Journal of Biological Chemistry, vol. 286, pp. 32586-92, 2011, ISSN: 1083-351X.

Abstract | Links

Stuart A Sievers, John Karanicolas, Howard W Chang, Anni Zhao, Lin Jiang, Onofrio Zirafi, Jason T Stevens, Jan M"unch, David Baker, David Eisenberg

Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation Journal Article

In: Nature, 2011, ISSN: 1476-4687.

Abstract | Links

Javier Guenaga, Pia Dosenovic, Gilad Ofek, David Baker, William R Schief, Peter D Kwong, Gunilla B Karlsson Hedestam, Richard T Wyatt

Heterologous epitope-scaffold prime:boosting immuno-focuses B cell responses to the HIV-1 gp41 2F5 neutralization determinant Journal Article

In: PloS one, vol. 6, pp. e16074, 2011, ISSN: 1932-6203.

Abstract

2010

Gilad Ofek, F Javier Guenaga, William R Schief, Jeff Skinner, David Baker, Richard Wyatt, Peter D Kwong

Elicitation of structure-specific antibodies by epitope scaffolds Journal Article

In: Proceedings of the National Academy of Sciences of the United States of America, vol. 107, pp. 17880-7, 2010, ISSN: 1091-6490.

Abstract

Bruno E Correia, Yih-En Andrew Ban, Margaret A Holmes, Hengyu Xu, Katharine Ellingson, Zane Kraft, Chris Carrico, Erica Boni, D Noah Sather, Camille Zenobia, Katherine Y Burke, Tyler Bradley-Hewitt, Jessica F Bruhn-Johannsen, Oleksandr Kalyuzhniy, David Baker, Roland K Strong, Leonidas Stamatatos, William R Schief

Computational design of epitope-scaffolds allows induction of antibodies specific for a poorly immunogenic HIV vaccine epitope Journal Article

In: Structure, vol. 18, pp. 1116-26, 2010, ISSN: 1878-4186.

Abstract

Douglas M Fowler, Carlos L Araya, Sarel J Fleishman, Elizabeth H Kellogg, Jason J Stephany, David Baker, Stanley Fields

High-resolution mapping of protein sequence-function relationships Journal Article

In: Nature methods, vol. 7, pp. 741-6, 2010, ISSN: 1548-7105.

Abstract

Ben Blum, Michael I Jordan, David Baker

Feature space resampling for protein conformational search Journal Article

In: Proteins, vol. 78, pp. 1583-93, 2010, ISSN: 1097-0134.

Abstract

Charles Chung Yun Leung, Elizabeth Kellogg, Anja Kuhnert, Frank H"anel, David Baker, J N Mark Glover

Insights from the crystal structure of the sixth BRCT domain of topoisomerase IIbeta binding protein 1 Journal Article

In: Protein science : a publication of the Protein Society, vol. 19, pp. 162-7, 2010, ISSN: 1469-896X.

Abstract | Links

2008

Christine McBeth, Audrey Seamons, Juan C Pizarro, Sarel J Fleishman, David Baker, Tanja Kortemme, Joan M Goverman, Roland K Strong

A new twist in TCR diversity revealed by a forbidden alphabeta TCR Journal Article

In: Journal of molecular biology, vol. 375, pp. 1306-19, 2008, ISSN: 1089-8638.

Abstract

2007

Ingemar Andr'e, Philip Bradley, Chu Wang, David Baker

Prediction of the structure of symmetrical protein assemblies Journal Article

In: Proceedings of the National Academy of Sciences of the United States of America, vol. 104, pp. 17656-61, 2007, ISSN: 0027-8424.

Abstract | Links

Kiril Tsemekhman, Lukasz Goldschmidt, David Eisenberg, David Baker

Cooperative hydrogen bonding in amyloid formation Journal Article

In: Protein science, vol. 16, pp. 761-4, 2007, ISSN: 0961-8368.

Abstract | Links

Alexander L Watters, Pritilekha Deka, Colin Corrent, David Callender, Gabriele Varani, Tobin Sosnick, David Baker

The highly cooperative folding of small naturally occurring proteins is likely the result of natural selection Journal Article

In: Cell, vol. 128, pp. 613-24, 2007, ISSN: 0092-8674.

Abstract

2006

Amy E Palmer, Marta Giacomello, Tanja Kortemme, S Andrew Hires, Varda Lev-Ram, David Baker, Roger Y Tsien

Ca2+ indicators based on computationally redesigned calmodulin-peptide pairs Journal Article

In: Chemistry & biology, vol. 13, pp. 521-30, 2006, ISSN: 1074-5521.

Abstract | Links

Vanita D Sood, David Baker

Recapitulation and design of protein binding peptide structures and sequences Journal Article

In: Journal of molecular biology, vol. 357, pp. 917-27, 2006, ISSN: 0022-2836.

Abstract | Links

Michael J Thompson, Stuart A Sievers, John Karanicolas, Magdalena I Ivanova, David Baker, David Eisenberg

The 3D profile method for identifying fibril-forming segments of proteins Journal Article

In: Proceedings of the National Academy of Sciences of the United States of America, vol. 103, pp. 4074-8, 2006, ISSN: 0027-8424.

Abstract | Links

49 entries « 1 of 2 »