Publications

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148 entries « 1 of 8 »
1.

Mansoor, Sanaa; Baek, Minkyung; Park, Hahnbeom; Lee, Gyu Rie; Baker, David

Protein Ensemble Generation Through Variational Autoencoder Latent Space Sampling Journal Article

In: J. Chem. Theory Comput., 2024.

Abstract | Links | BibTeX

2.

Krishna, Rohith; Wang, Jue; Ahern, Woody; Sturmfels, Pascal; Venkatesh, Preetham; Kalvet, Indrek; Lee, Gyu Rie; Morey-Burrows, Felix S.; Anishchenko, Ivan; Humphreys, Ian R.; McHugh, Ryan; Vafeados, Dionne; Li, Xinting; Sutherland, George A.; Hitchcock, Andrew; Hunter, C. Neil; Kang, Alex; Brackenbrough, Evans; Bera, Asim K.; Baek, Minkyung; DiMaio, Frank; Baker, David

Generalized biomolecular modeling and design with RoseTTAFold All-Atom Journal Article

In: Science, 2024.

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3.

Baek, Minkyung; McHugh, Ryan; Anishchenko, Ivan; Jiang, Hanlun; Baker, David; DiMaio, Frank

Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA Journal Article

In: Nature Methods, 2023.

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4.

Mansoor, Sanaa; Baek, Minkyung; Juergens, David; Watson, Joseph L.; Baker, David

Zero‐shot Mutation Effect Prediction on Protein Stability and Function using RoseTTAFold Journal Article

In: Protein Science, 2023.

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5.

Watson, Joseph L.; Juergens, David; Bennett, Nathaniel R.; Trippe, Brian L.; Yim, Jason; Eisenach, Helen E.; Ahern, Woody; Borst, Andrew J.; Ragotte, Robert J.; Milles, Lukas F.; Wicky, Basile I. M.; Hanikel, Nikita; Pellock, Samuel J.; Courbet, Alexis; Sheffler, William; Wang, Jue; Venkatesh, Preetham; Sappington, Isaac; Torres, Susana Vázquez; Lauko, Anna; De Bortoli, Valentin; Mathieu, Emile; Ovchinnikov, Sergey; Barzilay, Regina; Jaakkola, Tommi S.; DiMaio, Frank; Baek, Minkyung; Baker, David

De novo design of protein structure and function with RFdiffusion Journal Article

In: Nature, 2023.

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6.

Justas Dauparas Amir Motmaen, Minkyung Baek

Peptide-binding specificity prediction using fine-tuned protein structure prediction networks Journal Article

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

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7.

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.

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8.

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.

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9.

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.

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10.

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.

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11.

Baek, Minkyung; Baker, David

Deep learning and protein structure modeling Journal Article

In: Nature Methods, 2022.

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12.

Anishchenko, Ivan; Pellock, Samuel J.; Chidyausiku, Tamuka M.; Ramelot, Theresa A.; Ovchinnikov, Sergey; Hao, Jingzhou; Bafna, Khushboo; Norn, Christoffer; Kang, Alex; Bera, Asim K.; DiMaio, Frank; Carter, Lauren; Chow, Cameron M.; Montelione, Gaetano T.; Baker, David

De novo protein design by deep network hallucination Journal Article

In: Nature, 2021.

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13.

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.

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14.

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.

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15.

Baek, Minkyung; DiMaio, Frank; Anishchenko, Ivan; Dauparas, Justas; Ovchinnikov, Sergey; Lee, Gyu Rie; Wang, Jue; Cong, Qian; Kinch, Lisa N.; Schaeffer, R. Dustin; Millán, Claudia; Park, Hahnbeom; Adams, Carson; Glassman, Caleb R.; DeGiovanni, Andy; Pereira, Jose H.; Rodrigues, Andria V.; van Dijk, Alberdina A.; Ebrecht, Ana C.; Opperman, Diederik J.; Sagmeister, Theo; Buhlheller, Christoph; Pavkov-Keller, Tea; Rathinaswamy, Manoj K.; Dalwadi, Udit; Yip, Calvin K.; Burke, John E.; Garcia, K. Christopher; Grishin, Nick V.; Adams, Paul D.; Read, Randy J.; Baker, David

Accurate prediction of protein structures and interactions using a three-track neural network Journal Article

In: Science, 2021.

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16.

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.

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17.

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.

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18.

Park, Hahnbeom; Zhou, Guangfeng; Baek, Minkyung; Baker, David; DiMaio, Frank

Force Field Optimization Guided by Small Molecule Crystal Lattice Data Enables Consistent Sub-Angstrom Protein–Ligand Docking Journal Article

In: Journal of Chemical Theory and Computation, 2021.

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19.

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.

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20.

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

148 entries « 1 of 8 »