Publications

Preprints are available on bioRxiv.

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1.

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

2.

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

3.

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

4.

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

5.

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

6.

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

7.

Baek, Minkyung; Baker, David

Deep learning and protein structure modeling Journal Article

In: Nature Methods, 2022.

Abstract | Links | BibTeX

8.

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

9.

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

10.

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

11.

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

12.

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

13.

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

14.

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

 

2022

FROM THE LAB

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

Hallucinating symmetric protein assemblies Journal Article

In: Science, 2022.

Abstract | Links

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

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

In: Science, 2022.

Abstract | Links

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

Scaffolding protein functional sites using deep learning Journal Article

In: Science, 2022.

Abstract | Links

Minkyung Baek, David Baker

Deep learning and protein structure modeling Journal Article

In: Nature Methods, 2022.

Abstract | Links

COLLABORATOR LED

Show all

Sen, Neeladri and Anishchenko, Ivan and Bordin N and Sillitoe, Ian and Velankar, Sameer and Baker, David and 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

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

The road to fully programmable protein catalysis Journal Article

In: Nature, 2022.

Abstract | Links

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

2021

FROM THE LAB

Show all

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

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

In: Proteins, 2021.

Abstract | Links

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

COLLABORATOR LED

Show all

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

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

In: Nature Protocols, 2021.

Abstract | Links

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

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

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

Abstract | Links

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

2020

FROM THE LAB

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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

COLLABORATOR LED

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Sorry, no publications matched your criteria.

2019

FROM THE LAB

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COLLABORATOR LED

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

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

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

Abstract | Links

2018

FROM THE LAB

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COLLABORATOR LED

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2017–1998

ALL PAPERS

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