Effective gene expression prediction from sequence by integrating long-range interactions
Avsec, Žiga, Agarwal, Vikram, Visentin, Daniel, Ledsam, Joseph R., Grabska-Barwinska, Agnieszka, Taylor, Kyle R., Assael, Yannis, Jumper, John, Kohli, Pushmeet, Kelley, David R.
Published in Nature methods (01.10.2021)
Published in Nature methods (01.10.2021)
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Highly accurate protein structure prediction for the human proteome
Tunyasuvunakool, Kathryn, Adler, Jonas, Wu, Zachary, Green, Tim, Zielinski, Michal, Žídek, Augustin, Bridgland, Alex, Cowie, Andrew, Meyer, Clemens, Laydon, Agata, Velankar, Sameer, Kleywegt, Gerard J., Bateman, Alex, Evans, Richard, Pritzel, Alexander, Figurnov, Michael, Ronneberger, Olaf, Bates, Russ, Kohl, Simon A. A., Potapenko, Anna, Ballard, Andrew J., Romera-Paredes, Bernardino, Nikolov, Stanislav, Jain, Rishub, Clancy, Ellen, Reiman, David, Petersen, Stig, Senior, Andrew W., Kavukcuoglu, Koray, Birney, Ewan, Kohli, Pushmeet, Jumper, John, Hassabis, Demis
Published in Nature (London) (26.08.2021)
Published in Nature (London) (26.08.2021)
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Journal Article
Accurate structure prediction of biomolecular interactions with AlphaFold 3
Abramson, Josh, Adler, Jonas, Dunger, Jack, Evans, Richard, Green, Tim, Pritzel, Alexander, Ronneberger, Olaf, Willmore, Lindsay, Ballard, Andrew J., Bambrick, Joshua, Bodenstein, Sebastian W., Evans, David A., Hung, Chia-Chun, O’Neill, Michael, Reiman, David, Tunyasuvunakool, Kathryn, Wu, Zachary, Žemgulytė, Akvilė, Arvaniti, Eirini, Beattie, Charles, Bertolli, Ottavia, Bridgland, Alex, Cherepanov, Alexey, Congreve, Miles, Cowen-Rivers, Alexander I., Cowie, Andrew, Figurnov, Michael, Fuchs, Fabian B., Gladman, Hannah, Jain, Rishub, Khan, Yousuf A., Low, Caroline M. R., Perlin, Kuba, Potapenko, Anna, Savy, Pascal, Singh, Sukhdeep, Stecula, Adrian, Thillaisundaram, Ashok, Tong, Catherine, Yakneen, Sergei, Zhong, Ellen D., Zielinski, Michal, Žídek, Augustin, Bapst, Victor, Kohli, Pushmeet, Jaderberg, Max, Hassabis, Demis, Jumper, John M.
Published in Nature (London) (13.06.2024)
Published in Nature (London) (13.06.2024)
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Atomic-Level Characterization of the Structural Dynamics of Proteins
Shaw, David E, Maragakis, Paul, Lindorff-Larsen, Kresten, Piana, Stefano, Dror, Ron O, Eastwood, Michael P, Bank, Joseph A, Jumper, John M, Salmon, John K, Shan, Yibing, Wriggers, Willy
Published in Science (American Association for the Advancement of Science) (15.10.2010)
Published in Science (American Association for the Advancement of Science) (15.10.2010)
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Journal Article
Applying and improving AlphaFold at CASP14
Jumper, John, Evans, Richard, Pritzel, Alexander, Green, Tim, Figurnov, Michael, Ronneberger, Olaf, Tunyasuvunakool, Kathryn, Bates, Russ, Žídek, Augustin, Potapenko, Anna, Bridgland, Alex, Meyer, Clemens, Kohl, Simon A. A., Ballard, Andrew J., Cowie, Andrew, Romera‐Paredes, Bernardino, Nikolov, Stanislav, Jain, Rishub, Adler, Jonas, Back, Trevor, Petersen, Stig, Reiman, David, Clancy, Ellen, Zielinski, Michal, Steinegger, Martin, Pacholska, Michalina, Berghammer, Tamas, Silver, David, Vinyals, Oriol, Senior, Andrew W., Kavukcuoglu, Koray, Kohli, Pushmeet, Hassabis, Demis
Published in Proteins, structure, function, and bioinformatics (01.12.2021)
Published in Proteins, structure, function, and bioinformatics (01.12.2021)
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Journal Article
Protein structure prediction using multiple deep neural networks in the 13th Critical Assessment of Protein Structure Prediction (CASP13)
Senior, Andrew W., Evans, Richard, Jumper, John, Kirkpatrick, James, Sifre, Laurent, Green, Tim, Qin, Chongli, Žídek, Augustin, Nelson, Alexander W. R., Bridgland, Alex, Penedones, Hugo, Petersen, Stig, Simonyan, Karen, Crossan, Steve, Kohli, Pushmeet, Jones, David T., Silver, David, Kavukcuoglu, Koray, Hassabis, Demis
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
Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water
Riback, Joshua A., Bowman, Micayla A., Zmyslowski, Adam M., Knoverek, Catherine R., Jumper, John M., Hinshaw, James R., Kaye, Emily B., Freed, Karl F., Clark, Patricia L., Sosnick, Tobin R.
Published in Science (American Association for the Advancement of Science) (13.10.2017)
Published in Science (American Association for the Advancement of Science) (13.10.2017)
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Journal Article
Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations
Baxa, Michael C., Haddadian, Esmael J., Jumper, John M., Freed, Karl F., Sosnick, Tobin R.
Published in Proceedings of the National Academy of Sciences - PNAS (28.10.2014)
Published in Proceedings of the National Academy of Sciences - PNAS (28.10.2014)
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Journal Article
On the Interpretation of Force-Induced Unfolding Studies of Membrane Proteins Using Fast Simulations
Wang, Zongan, Jumper, John M., Freed, Karl F., Sosnick, Tobin R.
Published in Biophysical journal (15.10.2019)
Published in Biophysical journal (15.10.2019)
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Journal Article
Oncogenic Mutations Counteract Intrinsic Disorder in the EGFR Kinase and Promote Receptor Dimerization
Shan, Yibing, Eastwood, Michael P., Zhang, Xuewu, Kim, Eric T., Arkhipov, Anton, Dror, Ron O., Jumper, John, Kuriyan, John, Shaw, David E.
Published in Cell (11.05.2012)
Published in Cell (11.05.2012)
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Journal Article
A Membrane Burial Potential with H-Bonds and Applications to Curved Membranes and Fast Simulations
Wang, Zongan, Jumper, John M., Wang, Sheng, Freed, Karl F., Sosnick, Tobin R.
Published in Biophysical journal (20.11.2018)
Published in Biophysical journal (20.11.2018)
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Journal Article
Discovery of archaeal fusexins homologous to eukaryotic HAP2/GCS1 gamete fusion proteins
Moi, David, Nishio, Shunsuke, Li, Xiaohui, Valansi, Clari, Langleib, Mauricio, Brukman, Nicolas G., Flyak, Kateryna, Dessimoz, Christophe, de Sanctis, Daniele, Tunyasuvunakool, Kathryn, Jumper, John, Graña, Martin, Romero, Héctor, Aguilar, Pablo S., Jovine, Luca, Podbilewicz, Benjamin
Published in Nature communications (06.07.2022)
Published in Nature communications (06.07.2022)
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Journal Article
Free-Standing Kinked Silicon Nanowires for Probing Inter- and Intracellular Force Dynamics
Zimmerman, John F, Murray, Graeme F, Wang, Yucai, Jumper, John M, Austin, Jotham R, Tian, Bozhi
Published in Nano letters (12.08.2015)
Published in Nano letters (12.08.2015)
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Journal Article
Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase
Fraser, Alec, Sokolova, Maria L., Drobysheva, Arina V., Gordeeva, Julia V., Borukhov, Sergei, Jumper, John, Severinov, Konstantin V., Leiman, Petr G.
Published in Nature communications (20.06.2022)
Published in Nature communications (20.06.2022)
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Journal Article
Structure of the PAPP-ABP5 complex reveals mechanism of substrate recognition
Judge, Russell A., Sridar, Janani, Tunyasuvunakool, Kathryn, Jain, Rinku, Wang, John C. K., Ouch, Christna, Xu, Jun, Mafi, Amirhossein, Nile, Aaron H., Remarcik, Clint, Smith, Corey L., Ghosh, Crystal, Xu, Chen, Stoll, Vincent, Jumper, John, Singh, Amoolya H., Eaton, Dan, Hao, Qi
Published in Nature communications (20.09.2022)
Published in Nature communications (20.09.2022)
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Journal Article
Author Correction: Structure of the PAPP-ABP5 complex reveals mechanism of substrate recognition
Judge, Russell A., Sridar, Janani, Tunyasuvunakool, Kathryn, Jain, Rinku, Wang, John C. K., Ouch, Christna, Xu, Jun, Mafi, Amirhossein, Nile, Aaron H., Remarcik, Clint, Smith, Corey L., Ghosh, Crystal, Xu, Chen, Stoll, Vincent, Jumper, John, Singh, Amoolya H., Eaton, Dan, Hao, Qi
Published in Nature communications (28.09.2022)
Published in Nature communications (28.09.2022)
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