Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments by Park, Hahnbeom, Lee, Gyu Rie, Heo, Lim, Seok, Chaok

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High‐accuracy refinement using Rosetta in CASP13 by Park, Hahnbeom, Lee, Gyu Rie, Kim, David E., Anishchenko, Ivan, Cong, Qian, Baker, David

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Generalized biomolecular modeling and design with RoseTTAFold All-Atom by 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

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De novo design of luciferases using deep learning by 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

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

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Simultaneous refinement of inaccurate local regions and overall structure in the CASP12 protein model refinement experiment by Lee, Gyu Rie, Heo, Lim, Seok, Chaok

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De novo design of high-affinity binders of bioactive helical peptides by Vázquez Torres, Susana, Leung, Philip J. Y., Venkatesh, Preetham, Lutz, Isaac D., Hink, Fabian, Huynh, Huu-Hien, Becker, Jessica, Yeh, Andy Hsien-Wei, Juergens, David, Bennett, Nathaniel R., Hoofnagle, Andrew N., Huang, Eric, MacCoss, Michael J., Expòsit, Marc, Lee, Gyu Rie, Bera, Asim K., Kang, Alex, De La Cruz, Joshmyn, Levine, Paul M., Li, Xinting, Lamb, Mila, Gerben, Stacey R., Murray, Analisa, Heine, Piper, Korkmaz, Elif Nihal, Nivala, Jeff, Stewart, Lance, Watson, Joseph L., Rogers, Joseph M., Baker, David

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Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment by Lensink, Marc F., Velankar, Sameer, Kryshtafovych, Andriy, Huang, Shen-You, Schneidman-Duhovny, Dina, Segura, Joan, Fernandez-Fuentes, Narcis, Viswanath, Shruthi, Elber, Ron, Grudinin, Sergei, Popov, Petr, Neveu, Emilie, Lee, Hasup, Baek, Minkyung, Park, Sangwoo, Heo, Lim, Rie Lee, Gyu, Seok, Chaok, Qin, Sanbo, Zhou, Huan-Xiang, Ritchie, David W., Maigret, Bernard, Devignes, Marie-Dominique, Ghoorah, Anisah, Torchala, Mieczyslaw, Chaleil, Raphaël A.G., Bates, Paul A., Ben-Zeev, Efrat, Eisenstein, Miriam, Negi, Surendra S., Weng, Zhiping, Vreven, Thom, Pierce, Brian G., Borrman, Tyler M., Yu, Jinchao, Ochsenbein, Françoise, Guerois, Raphaël, Vangone, Anna, Rodrigues, João P.G.L.M., van Zundert, Gydo, Nellen, Mehdi, Xue, Li, Karaca, Ezgi, Melquiond, Adrien S.J., Visscher, Koen, Kastritis, Panagiotis L., Bonvin, Alexandre M.J.J., Xu, Xianjin, Qiu, Liming, Yan, Chengfei, Li, Jilong, Ma, Zhiwei, Cheng, Jianlin, Zou, Xiaoqin, Shen, Yang, Peterson, Lenna X., Kim, Hyung-Rae, Roy, Amit, Han, Xusi, Esquivel-Rodriguez, Juan, Kihara, Daisuke, Yu, Xiaofeng, Bruce, Neil J., Fuller, Jonathan C., Wade, Rebecca C., Anishchenko, Ivan, Kundrotas, Petras J., Vakser, Ilya A., Imai, Kenichiro, Yamada, Kazunori, Oda, Toshiyuki, Nakamura, Tsukasa, Tomii, Kentaro, Pallara, Chiara, Romero-Durana, Miguel, Jiménez-García, Brian, Moal, Iain H., Férnandez-Recio, Juan, Joung, Jong Young, Kim, Jong Yun, Joo, Keehyoung, Lee, Jooyoung, Kozakov, Dima, Vajda, Sandor, Mottarella, Scott, Hall, David R., Beglov, Dmitri, Mamonov, Artem, Xia, Bing, Bohnuud, Tanggis, Del Carpio, Carlos A., Ichiishi, Eichiro, Marze, Nicholas, Kuroda, Daisuke, Gray, Jeffrey J., Chermak, Edrisse, Cavallo, Luigi, Oliva, Romina, Tovchigrechko, Andrey, Wodak, Shoshana J.

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Template‐based modeling and ab initio refinement of protein oligomer structures using GALAXY in CAPRI round 30 by Lee, Hasup, Baek, Minkyung, Lee, Gyu Rie, Park, Sangwoo, Seok, Chaok

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Biophysical and functional characterization of Norrin signaling through Frizzled4 by Bang, Injin, Kim, Hee Ryung, Beaven, Andrew H., Kim, Jinuk, Ko, Seung-Bum, Lee, Gyu Rie, Lee, Hasup, Im, Wonpil, Seok, Chaok, Chung, Ka Young, Choi, Hee-Jung

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Binding and sensing diverse small molecules using shape-complementary pseudocycles by An, Linna, Said, Meerit, Tran, Long, Majumder, Sagardip, Goreshnik, Inna, Lee, Gyu Rie, Juergens, David, Dauparas, Justas, Anishchenko, Ivan, Coventry, Brian, Bera, Asim K, Kang, Alex, Levine, Paul M, Alvarez, Valentina, Pillai, Arvind, Norn, Christoffer, Feldman, David, Zorine, Dmitri, Hicks, Derrick R, Li, Xinting, Sanchez, Mariana Garcia, Vafeados, Dionne K, Salveson, Patrick J, Vorobieva, Anastassia A, Baker, David

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Evaluating GPCR modeling and docking strategies in the era of deep learning-based protein structure prediction by Lee, Sumin, Kim, Seeun, Lee, Gyu Rie, Kwon, Sohee, Woo, Hyeonuk, Seok, Chaok, Park, Hahnbeom

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An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12 by Keasar, Chen, McGuffin, Liam J., Wallner, Björn, Chopra, Gaurav, Adhikari, Badri, Bhattacharya, Debswapna, Blake, Lauren, Bortot, Leandro Oliveira, Cao, Renzhi, Dhanasekaran, B. K., Dimas, Itzhel, Faccioli, Rodrigo Antonio, Faraggi, Eshel, Ganzynkowicz, Robert, Ghosh, Sambit, Ghosh, Soma, Giełdoń, Artur, Golon, Lukasz, He, Yi, Heo, Lim, Hou, Jie, Khan, Main, Khatib, Firas, Khoury, George A., Kieslich, Chris, Kim, David E., Krupa, Pawel, Lee, Gyu Rie, Li, Hongbo, Li, Jilong, Lipska, Agnieszka, Liwo, Adam, Maghrabi, Ali Hassan A., Mirdita, Milot, Mirzaei, Shokoufeh, Mozolewska, Magdalena A., Onel, Melis, Ovchinnikov, Sergey, Shah, Anand, Shah, Utkarsh, Sidi, Tomer, Sieradzan, Adam K., Ślusarz, Magdalena, Ślusarz, Rafal, Smadbeck, James, Tamamis, Phanourios, Trieber, Nicholas, Wirecki, Tomasz, Yin, Yanping, Zhang, Yang, Bacardit, Jaume, Baranowski, Maciej, Chapman, Nicholas, Cooper, Seth, Defelicibus, Alexandre, Flatten, Jeff, Koepnick, Brian, Popović, Zoran, Zaborowski, Bartlomiej, Baker, David, Cheng, Jianlin, Czaplewski, Cezary, Delbem, Alexandre Cláudio Botazzo, Floudas, Christodoulos, Kloczkowski, Andrzej, Ołdziej, Stanislaw, Levitt, Michael, Scheraga, Harold, Seok, Chaok, Söding, Johannes, Vishveshwara, Saraswathi, Xu, Dong, Crivelli, Silvia N.

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Effective protein model structure refinement by loop modeling and overall relaxation by Lee, Gyu Rie, Heo, Lim, Seok, Chaok

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Conformational Sampling of Flexible Ligand-binding Protein Loops by Lee, Gyu-Rie, Shin, Woong-Hee, Park, Hahn-Beom, Shin, Seok-Min, Seok, Cha-Ok

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GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure by Lee, Gyu Rie, Won, Jonghun, Heo, Lim, Seok, Chaok

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Galaxy7TM: flexible GPCR-ligand docking by structure refinement by Lee, Gyu Rie, Seok, Chaok

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Protein Ensemble Generation Through Variational Autoencoder Latent Space Sampling by Mansoor, Sanaa, Baek, Minkyung, Park, Hahnbeom, Lee, Gyu Rie, Baker, David

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GalaxyGPCRloop: Template-Based and Ab Initio Structure Sampling of the Extracellular Loops of G‑Protein-Coupled Receptors by Won, Jonghun, Lee, Gyu Rie, Park, Hahnbeom, Seok, Chaok

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CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods by Jain, Shantanu, Bakolitsa, Constantina, Brenner, Steven E., Radivojac, Predrag, Moult, John, Repo, Susanna, Hoskins, Roger A., Andreoletti, Gaia, Barsky, Daniel, Chellapan, Ajithavalli, Chu, Hoyin, Dabbiru, Navya, Kollipara, Naveen K., Ly, Melissa, Neumann, Andrew J., Pal, Lipika R., Odell, Eric, Pandey, Gaurav, Peters-Petrulewicz, Robin C., Srinivasan, Rajgopal, Yee, Stephen F., Yeleswarapu, Sri Jyothsna, Zuhl, Maya, Adebali, Ogun, Patra, Ayoti, Beer, Michael A., Hosur, Raghavendra, Peng, Jian, Bernard, Brady M., Berry, Michael, Dong, Shengcheng, Boyle, Alan P., Adhikari, Aashish, Chen, Jingqi, Hu, Zhiqiang, Wang, Robert, Wang, Yaqiong, Miller, Maximilian, Wang, Yanran, Bromberg, Yana, Turina, Paola, Capriotti, Emidio, Han, James J., Ozturk, Kivilcim, Carter, Hannah, Babbi, Giulia, Bovo, Samuele, Di Lena, Pietro, Martelli, Pier Luigi, Savojardo, Castrense, Casadio, Rita, Cline, Melissa S., De Baets, Greet, Bonache, Sandra, Díez, Orland, Gutiérrez-Enríquez, Sara, Fernández, Alejandro, Montalban, Gemma, Ootes, Lars, Özkan, Selen, Padilla, Natàlia, Riera, Casandra, De la Cruz, Xavier, Diekhans, Mark, Huwe, Peter J., Wei, Qiong, Xu, Qifang, Dunbrack, Roland L., Gotea, Valer, Elnitski, Laura, Margolin, Gennady, Fariselli, Piero, Kulakovskiy, Ivan V., Makeev, Vsevolod J., Penzar, Dmitry D., Vorontsov, Ilya E., Favorov, Alexander V., Forman, Julia R., Hasenahuer, Marcia, Fornasari, Maria S., Parisi, Gustavo, Avsec, Ziga, Çelik, Muhammed H., Nguyen, Thi Yen Duong, Gagneur, Julien, Shi, Fang-Yuan, Edwards, Matthew D., Guo, Yuchun, Tian, Kevin, Zeng, Haoyang, Gifford, David K., Göke, Jonathan, Zaucha, Jan, Gough, Julian, Ritchie, Graham R. S., Frankish, Adam, Mudge, Jonathan M., Harrow, Jennifer, Young, Erin L., Yu, Yao

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