Publications

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1.

Bennett, Nathaniel R.; Coventry, Brian; Goreshnik, Inna; Huang, Buwei; Allen, Aza; Vafeados, Dionne; Peng, Ying Po; Dauparas, Justas; Baek, Minkyung; Stewart, Lance; DiMaio, Frank; De Munck, Steven; Savvides, Savvas N.; Baker, David

Improving de novo protein binder design with deep learning Journal Article

In: Nature Communications, 2023.

Abstract | Links | BibTeX

2.

Kim, David E.; Jensen, Davin R.; Feldman, David; Tischer, Doug; Saleem, Ayesha; Chow, Cameron M.; Li, Xinting; Carter, Lauren; Milles, Lukas; Nguyen, Hannah; Kang, Alex; Bera, Asim K.; Peterson, Francis C.; Volkman, Brian F.; Ovchinnikov, Sergey; Baker, David

De novo design of small beta barrel proteins Journal Article

In: Proceedings of the National Academy of Sciences, 2023.

Abstract | Links | BibTeX

3.

Andy Hsien-Wei Norn Yeh, Christoffer Kipnis

De novo design of luciferases using deep learning Journal Article

In: Nature, 2023.

Abstract | Links | BibTeX

4.

Wicky, B. I. M.; Milles, L. F.; Courbet, A.; Ragotte, R. J.; Dauparas, J.; Kinfu, E.; Tipps, S.; Kibler, R. D.; Baek, M.; DiMaio, F.; Li, X.; Carter, L.; Kang, A.; Nguyen, H.; Bera, A. K.; Baker, D.

Hallucinating symmetric protein assemblies Journal Article

In: Science, 2022.

Abstract | Links | BibTeX

5.

Dauparas, J.; Anishchenko, I.; Bennett, N.; Bai, H.; Ragotte, R. J.; Milles, L. F.; Wicky, B. I. M.; Courbet, A.; de Haas, R. J.; Bethel, N.; Leung, P. J. Y.; Huddy, T. F.; Pellock, S.; Tischer, D.; Chan, F.; Koepnick, B.; Nguyen, H.; Kang, A.; Sankaran, B.; Bera, A. K.; King, N. P.; Baker, D.

Robust deep learning–based protein sequence design using ProteinMPNN Journal Article

In: Science, 2022.

Abstract | Links | BibTeX

6.

Wang, Jue; Lisanza, Sidney; Juergens, David; Tischer, Doug; Watson, Joseph L.; Castro, Karla M.; Ragotte, Robert; Saragovi, Amijai; Milles, Lukas F.; Baek, Minkyung; Anishchenko, Ivan; Yang, Wei; Hicks, Derrick R.; Expòsit, Marc; Schlichthaerle, Thomas; Chun, Jung-Ho; Dauparas, Justas; Bennett, Nathaniel; Wicky, Basile I. M.; Muenks, Andrew; DiMaio, Frank; Correia, Bruno; Ovchinnikov, Sergey; Baker, David

Scaffolding protein functional sites using deep learning Journal Article

In: Science, 2022.

Abstract | Links | BibTeX

7.

Sen, Neeladri; Anishchenko, Ivan; N, Bordin; Sillitoe, Ian; Velankar, Sameer; Baker, David; Orengo, Christine

Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs Journal Article

In: Briefings in Bioinformatics, 2022.

Abstract | Links | BibTeX

8.

Lovelock, Sarah L.; Crawshaw, Rebecca; Basler, Sophie; Levy, Colin; Baker, David; Hilvert, Donald; Green, Anthony P.

The road to fully programmable protein catalysis Journal Article

In: Nature, 2022.

Abstract | Links | BibTeX

9.

Linder, Johannes; La Fleur, Alyssa; Chen, Zibo; Ljubetič, Ajasja; Baker, David; Kannan, Sreeram; Seelig, Georg

Interpreting neural networks for biological sequences by learning stochastic masks Journal Article

In: Nature Machine Intelligence, 2022.

Abstract | Links | BibTeX

10.

Baek, Minkyung; Baker, David

Deep learning and protein structure modeling Journal Article

In: Nature Methods, 2022.

Abstract | Links | BibTeX

11.

Du, Zongyang; Su, Hong; Wang, Wenkai; Ye, Lisha; Wei, Hong; Peng, Zhenling; Anishchenko, Ivan; Baker, David; Yang, Jianyi

The trRosetta server for fast and accurate protein structure prediction Journal Article

In: Nature Protocols, 2021.

Abstract | Links | BibTeX

12.

Baek, Minkyung; Anishchenko, Ivan; Park, Hahnbeom; Humphreys, Ian R.; Baker, David

Protein oligomer modeling guided by predicted inter-chain contacts in CASP14 Journal Article

In: Proteins, 2021.

Abstract | Links | BibTeX

13.

Norn, Christoffer; Wicky, Basile I. M.; Juergens, David; Liu, Sirui; Kim, David; Tischer, Doug; Koepnick, Brian; Anishchenko, Ivan; Baker, David; Ovchinnikov, Sergey

Protein sequence design by conformational landscape optimization Journal Article

In: Proceedings of the National Academy of Sciences, vol. 118, no. 11, 2021.

Abstract | Links | BibTeX

14.

Hiranuma, Naozumi; Park, Hahnbeom; Baek, Minkyung; Anishchenko, Ivan; Dauparas, Justas; Baker, David

Improved protein structure refinement guided by deep learning based accuracy estimation Journal Article

In: Nature Communications, vol. 12, no. 1340, 2021.

Abstract | Links | BibTeX

15.

Ziatdinov, Maxim; Zhang, Shuai; Dollar, Orion; Pfaendtner, Jim; Mundy, Christopher J.; Li, Xin; Pyles, Harley; Baker, David; De Yoreo, James J.; Kalinin, Sergei V.

Quantifying the Dynamics of Protein Self-Organization Using Deep Learning Analysis of Atomic Force Microscopy Data Journal Article

In: Nano Letters, 2021.

Abstract | Links | BibTeX

16.

Yang, Jianyi; Anishchenko, Ivan; Park, Hahnbeom; Peng, Zhenling; Ovchinnikov, Sergey; Baker, David

Improved protein structure prediction using predicted interresidue orientations Journal Article

In: Proceedings of the National Academy of Sciences, 2020, ISBN: 0027-8424.

Abstract | Links | BibTeX

17.

Wu, Qi; Peng, Zhenling; Anishchenko, Ivan; Cong, Qian; Baker, David; Yang, Jianyi

Protein contact prediction using metagenome sequence data and residual neural networks Journal Article

In: Bioinformatics, vol. 36, no. 1, 2019.

Abstract | Links | BibTeX