Publications

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1.

Davila-Hernandez, Fatima A; Jin, Biao; Pyles, Harley; Zhang, Shuai; Wang, Zheming; Huddy, Timothy F; Bera, Asim K; Kang, Alex; Chen, Chun-Long; Yoreo, James J De; Baker, David

Directing polymorph specific calcium carbonate formation with de novo protein templates Journal Article

In: Nature Communications, vol. 14, no. 1, pp. 8191, 2023, ISSN: 2041-1723.

Abstract | Links | BibTeX

2.

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

3.

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

Protein interaction networks revealed by proteome coevolution Journal Article

In: Science, 2019.

Abstract | Links | BibTeX

4.

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

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

In: Nature, 2019.

Abstract | Links | BibTeX

5.

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

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

Abstract | Links | BibTeX

6.

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

In: Proteins, 2015.

Abstract | Links | BibTeX

7.

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

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

Abstract | Links | BibTeX

8.

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

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

Abstract | Links | BibTeX

9.

Demers, Jean-Philippe; Habenstein, Birgit; Loquet, Antoine; Vasa, Suresh Kumar; Giller, Karin; Becker, Stefan; Baker, David; Lange, Adam; Sgourakis, Nikolaos G

High-resolution structure of the Shigella type-III secretion needle by solid-state NMR and cryo-electron microscopy. Journal Article

In: Nature communications, vol. 5, pp. 4976, 2014, ISSN: 2041-1723.

Abstract | Links | BibTeX

10.

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

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 | BibTeX

11.

Loquet, Antoine; Sgourakis, Nikolaos G; Gupta, Rashmi; Giller, Karin; Riedel, Dietmar; Goosmann, Christian; Griesinger, Christian; Kolbe, Michael; Baker, David; Becker, Stefan; Lange, Adam

Atomic model of the type III secretion system needle Journal Article

In: Nature, 2012.

Abstract | Links | BibTeX

12.

Raman, Srivatsan; Huang, Yuanpeng J; Mao, Binchen; Rossi, Paolo; Aramini, James M; Liu, Gaohua; Montelione, Gaetano T; Baker, David

Accurate automated protein NMR structure determination using unassigned NOESY data Journal Article

In: Journal of the American Chemical Society, vol. 132, pp. 202-7, 2010, ISSN: 1520-5126.

Abstract | BibTeX

13.

Luo, Bing-Hao; Karanicolas, John; Harmacek, Laura D; Baker, David; Springer, Timothy A

Rationally designed integrin beta3 mutants stabilized in the high affinity conformation Journal Article

In: The Journal of biological chemistry, vol. 284, pp. 3917-24, 2009, ISSN: 0021-9258.

Abstract | BibTeX

14.

Baker, Matthew L; Jiang, Wen; Wedemeyer, William J; Rixon, Frazer J; Baker, David; Chiu, Wah

Ab initio modeling of the herpesvirus VP26 core domain assessed by CryoEM density Journal Article

In: PLoS computational biology, vol. 2, pp. e146, 2006, ISSN: 1553-7358.

Abstract | Links | BibTeX

15.

Kim, David E; Chivian, Dylan; Malmstr"om, Lars; Baker, David

Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM Journal Article

In: Proteins, vol. 61 Suppl 7, pp. 193-200, 2005, ISSN: 1097-0134.

Abstract | Links | BibTeX

16.

Hazbun, Tony R; Malmstr"om, Lars; Anderson, Scott; Graczyk, Beth J; Fox, Bethany; Riffle, Michael; Sundin, Bryan A; Aranda, J Derringer; McDonald, W Hayes; Chiu, Chun-Hwei; Snydsman, Brian E; Bradley, Phillip; Muller, Eric G D; Fields, Stanley; Baker, David; Yates, John R; Davis, Trisha N

Assigning function to yeast proteins by integration of technologies Journal Article

In: Molecular cell, vol. 12, pp. 1353-65, 2003, ISSN: 1097-2765.

Abstract | Links | BibTeX

17.

Alm, Eric; Morozov, Alexandre V; Kortemme, Tanja; Baker, David

Simple physical models connect theory and experiment in protein folding kinetics Journal Article

In: Journal of molecular biology, vol. 322, pp. 463-76, 2002, ISSN: 0022-2836.

Abstract | Links | BibTeX