The trRosetta server for fast and accurate protein structure prediction
Du, Zongyang, Su, Hong, Wang, Wenkai, Ye, Lisha, Wei, Hong, Peng, Zhenling, Anishchenko, Ivan, Baker, David, Yang, Jianyi
Published in Nature protocols (01.12.2021)
Published in Nature protocols (01.12.2021)
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Journal Article
Improved protein structure refinement guided by deep learning based accuracy estimation
Hiranuma, Naozumi, Park, Hahnbeom, Baek, Minkyung, Anishchenko, Ivan, Dauparas, Justas, Baker, David
Published in Nature communications (26.02.2021)
Published in Nature communications (26.02.2021)
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Journal Article
Computed structures of core eukaryotic protein complexes
Humphreys, Ian R, Pei, Jimin, Baek, Minkyung, Krishnakumar, Aditya, Anishchenko, Ivan, Ovchinnikov, Sergey, Zhang, Jing, Ness, Travis J, Banjade, Sudeep, Bagde, Saket R, Stancheva, Viktoriya G, Li, Xiao-Han, Liu, Kaixian, Zheng, Zhi, Barrero, Daniel J, Roy, Upasana, Kuper, Jochen, Fernández, Israel S, Szakal, Barnabas, Branzei, Dana, Rizo, Josep, Kisker, Caroline, Greene, Eric C, Biggins, Sue, Keeney, Scott, Miller, Elizabeth A, Fromme, J Christopher, Hendrickson, Tamara L, Cong, Qian, Baker, David
Published in Science (American Association for the Advancement of Science) (10.12.2021)
Published in Science (American Association for the Advancement of Science) (10.12.2021)
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Journal Article
De novo design of luciferases using deep learning
Yeh, Andy Hsien-Wei, Norn, Christoffer, Kipnis, Yakov, Tischer, Doug, Pellock, Samuel J, Evans, Declan, Ma, Pengchen, Lee, Gyu Rie, Zhang, Jason Z, Anishchenko, Ivan, Coventry, Brian, Cao, Longxing, Dauparas, Justas, Halabiya, Samer, DeWitt, Michelle, Carter, Lauren, Houk, K N, Baker, David
Published in Nature (London) (23.02.2023)
Published in Nature (London) (23.02.2023)
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Journal Article
High‐accuracy refinement using Rosetta in CASP13
Park, Hahnbeom, Lee, Gyu Rie, Kim, David E., Anishchenko, Ivan, Cong, Qian, Baker, David
Published in Proteins, structure, function, and bioinformatics (01.12.2019)
Published in Proteins, structure, function, and bioinformatics (01.12.2019)
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Journal Article
Dockground: A comprehensive data resource for modeling of protein complexes
Kundrotas, Petras J., Anishchenko, Ivan, Dauzhenka, Taras, Kotthoff, Ian, Mnevets, Daniil, Copeland, Matthew M., Vakser, Ilya A.
Published in Protein science (01.01.2018)
Published in Protein science (01.01.2018)
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Journal Article
In silico detection of SARS-CoV-2 specific B-cell epitopes and validation in ELISA for serological diagnosis of COVID-19
Phan, Isabelle Q, Subramanian, Sandhya, Kim, David, Murphy, Michael, Pettie, Deleah, Carter, Lauren, Anishchenko, Ivan, Barrett, Lynn K, Craig, Justin, Tillery, Logan, Shek, Roger, Harrington, Whitney E, Koelle, David M, Wald, Anna, Veesler, David, King, Neil, Boonyaratanakornkit, Jim, Isoherranen, Nina, Greninger, Alexander L, Jerome, Keith R, Chu, Helen, Staker, Bart, Stewart, Lance, Myler, Peter J, Van Voorhis, Wesley C
Published in Scientific reports (22.02.2021)
Published in Scientific reports (22.02.2021)
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Journal Article
Structural basis for autophagy inhibition by the human Rubicon–Rab7 complex
Bhargava, Hersh K., Tabata, Keisuke, Byck, Jordan M., Hamasaki, Maho, Farrell, Daniel P., Anishchenko, Ivan, DiMaio, Frank, Im, Young Jun, Yoshimori, Tamotsu, Hurley, James H.
Published in Proceedings of the National Academy of Sciences - PNAS (21.07.2020)
Published in Proceedings of the National Academy of Sciences - PNAS (21.07.2020)
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Journal Article
Modeling complexes of modeled proteins
Anishchenko, Ivan, Kundrotas, Petras J., Vakser, Ilya A.
Published in Proteins, structure, function, and bioinformatics (01.03.2017)
Published in Proteins, structure, function, and bioinformatics (01.03.2017)
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Journal Article
Modeling CAPRI targets 110‐120 by template‐based and free docking using contact potential and combined scoring function
Kundrotas, Petras J., Anishchenko, Ivan, Badal, Varsha D., Das, Madhurima, Dauzhenka, Taras, Vakser, Ilya A.
Published in Proteins, structure, function, and bioinformatics (01.03.2018)
Published in Proteins, structure, function, and bioinformatics (01.03.2018)
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Journal Article
Deep learning enables the atomic structure determination of the Fanconi Anemia core complex from cryoEM
Farrell, Daniel P, Anishchenko, Ivan, Shakeel, Shabih, Lauko, Anna, Passmore, Lori A, Baker, David, DiMaio, Frank
Published in IUCrJ (01.09.2020)
Published in IUCrJ (01.09.2020)
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Journal Article
Hydrophobic amino acids in the hinge region of the 5A apolipoprotein mimetic peptide are essential for promoting cholesterol efflux by the ABCA1 transporter
Sviridov, Denis O, Andrianov, Alexander M, Anishchenko, Ivan V, Stonik, John A, Amar, Marcelo J A, Turner, Scott, Remaley, Alan T
Published in The Journal of pharmacology and experimental therapeutics (01.01.2013)
Published in The Journal of pharmacology and experimental therapeutics (01.01.2013)
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Journal Article
Structural analysis of the envelope gp120 V3 loop for some HIV-1 variants circulating in the countries of Eastern Europe
Andrianov, Alexander M., Kornoushenko, Yuri V., Anishchenko, Ivan V., Eremin, Vladimir F., Tuzikov, Alexander V.
Published in Journal of biomolecular structure & dynamics (01.07.2013)
Published in Journal of biomolecular structure & dynamics (01.07.2013)
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Journal Article
Accurate prediction of protein-nucleic acid complexes using RoseTTAFoldNA
Baek, Minkyung, McHugh, Ryan, Anishchenko, Ivan, Jiang, Hanlun, Baker, David, DiMaio, Frank
Published in Nature methods (01.01.2024)
Published in Nature methods (01.01.2024)
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Journal Article
Protein contact prediction using metagenome sequence data and residual neural networks
Wu, Qi, Peng, Zhenling, Anishchenko, Ivan, Cong, Qian, Baker, David, Yang, Jianyi
Published in Bioinformatics (01.01.2020)
Published in Bioinformatics (01.01.2020)
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