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Geometric deep learning improves generalizability of MHC-bound peptide predictions Marzella, Dario F.; Crocioni, Giulia; Radusinovic, Tadija; Lepikhov, Daniil; Severin, Heleen; Bodor, Dani L.; Rademaker, Daniel T.; Lin, Chiayu; Georgievska, Sonja; Renaud, Nicolas; Kessler, Amy L.; Lopez-Tarifa, Pablo; Buschow, Sonja I.; Bekkers, Erik; Xue, Li C. 分享 收藏
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PANDORA: A Fast, Anchor-Restrained Modelling Protocol for Peptide: MHC Complexes Marzella, Dario F.; Parizi, Farzaneh M.; Van Tilborg, Derek; Renaud, Nicolas; Sybrandi, Daan; Buzatu, Rafaella; Rademaker, Daniel T.; 't Hoen, Peter A. C.; Xue, Li C. 分享 收藏
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An overview of data-driven HADDOCK strategies in CAPRI rounds 38-45 Koukos, Panagiotis I.; Roel-Touris, Jorge; Ambrosetti, Francesco; Geng, Cunliang; Schaarschmidt, Jorg; Trellet, Mikael E.; Melquiond, Adrien S. J.; Xue, Li C.; Honorato, Rodrigo V.; Moreira, Irina; Kurkcuoglu, Zeynep; Vangone, Anna; Bonvin, Alexandre M. J. J. 分享 收藏
Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment Lensink, Marc F.; Brysbaert, Guillaume; Nadzirin, Nurul; Velankar, Sameer; Chaleil, Raphael A. G.; Gerguri, Tereza; Bates, Paul A.; Laine, Elodie; Carbone, Alessandra; Grudinin, Sergei; Kong, Ren; Liu, Ran-Ran; Xu, Xi-Ming; Shi, Hang; Chang, Shan; Eisenstein, Miriam; Karczynska, Agnieszka; Czaplewski, Cezary; Lubecka, Emilia; Lipska, Agnieszka; Krupa, Pawel; Mozolewska, Magdalena; Golon, Lukasz; Samsonov, Sergey; Liwo, Adam; Crivelli, Silvia; Pages, Guillaume; Karasikov, Mikhail; Kadukova, Maria; Yan, Yumeng; Huang, Sheng-You; Rosell, Mireia; Rodriguez-Lumbreras, Luis A.; Romero-Durana, Miguel; Diaz-Bueno, Lucia; Fernandez-Recio, Juan; Christoffer, Charles; Terashi, Genki; Shin, Woong-Hee; Aderinwale, Tunde; Maddhuri Venkata Subraman, Sai Raghavendra; Kihara, Daisuke; Kozakov, Dima; Vajda, Sandor; Porter, Kathryn; Padhorny, Dzmitry; Desta, Israel; Beglov, Dmitri; Ignatov, Mikhail; Kotelnikov, Sergey; Moal, Iain H.; Ritchie, David W.; de Beauchene, Isaure Chauvot; Maigret, Bernard; Devignes, Marie-Dominique; Echartea, Maria E. Ruiz; Barradas-Bautista, Didier; Cao, Zhen; Cavallo, Luigi; Oliva, Romina; Cao, Yue; Shen, Yang; Baek, Minkyung; Park, Taeyong; Woo, Hyeonuk; Seok, Chaok; Braitbard, Merav; Bitton, Lirane; Scheidman-Duhovny, Dina; Dapkunas, Justas; Olechnovic, Kliment; Venclovas, Ceslovas; Kundrotas, Petras J.; Belkin, Saveliy; Chakravarty, Devlina; Badal, Varsha D.; Vakser, Ilya A.; Vreven, Thom; Vangaveti, Sweta; Borrman, Tyler; Weng, Zhiping; Guest, Johnathan D.; Gowthaman, Ragul; Pierce, Brian G.; Xu, Xianjin; Duan, Rui; Qiu, Liming; Hou, Jie; Merideth, Benjamin Ryan; Ma, Zhiwei; Cheng, Jianlin; Zou, Xiaoqin; Koukos, Panos I.; Roel-Touris, Jorge; Ambrosetti, Francesco; Geng, Cunliang; Schaarschmidt, Jorg; Trellet, Mikael E.; Melquiond, Adrien S. J.; Xue, Li; Jimenez-Garcia, Brian; van Noort, Charlotte W.; Honorato, Rodrigo V.; Bonvin, Alexandre M. J. J.; Wodak, Shoshana J. 分享 收藏
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Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2 Kurkcuoglu, Zeynep; Koukos, Panagiotis I.; Citro, Nevia; Trellet, Mikael E.; Rodrigues, J. P. G. L. M.; Moreira, Irina S.; Roel-Touris, Jorge; Melquiond, Adrien S. J.; Geng, Cunliang; Schaarschmidt, Jorg; Xue, Li C.; Vangone, Anna; Bonvin, A. M. J. J. 分享 收藏
Sense and Simplicity in HADDOCK Scoring: Lessons from CASP-CAPRI (page 418) (vol 85, pg 417, 2017) Vangone, A.; Rodrigues, J. P. G. L. M.; Xue, L. C.; van Zundert, G. C. P.; Geng, C.; Kurkcuoglu, Z.; Nellen, M.; Narasimhan, S.; Karaca, E.; van Dijk, M.; Melquiond, A. S. J.; Visscher, K. M.; Trellet, M.; Kastritis, P. L.; Bonvin, A. M. J. J. 分享 收藏
Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1 Vangone, A.; Rodrigues, J. P. G. L. M.; Xue, L. C.; van Zundert, G. C. P.; Geng, C.; Kurkcuoglu, Z.; Nellen, M.; Narasimhan, S.; Karaca, E.; van Dijk, M.; Melquiond, A. S. J.; Visscher, K. M.; Trellet, M.; Kastritis, P. L.; Bonvin, A. M. J. J. 分享 收藏
Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment 通过蛋白质对接和基于模板的建模预测同蛋白和异蛋白复合物: casp-capri实验 Lensink, Marc F.; Velankar, Sameer; Kryshtafovych, Andriy; Huang, Shen-You; Schneidman-Duhovny, Dina; Sali, Andrej; Segura, Joan; Fernandez-Fuentes, Narcis; Viswanath, Shruthi; Elber, Ron; Grudinin, Sergei; Popov, Petr; Neveu, Emilie; Lee, Hasup; Baek, Minkyung; Park, Sangwoo; Heo, Lim; Lee, Gyu Rie; Seok, Chaok; Qin, Sanbo; Zhou, Huan-Xiang; Ritchie, David W.; Maigret, Bernard; Devignes, Marie-Dominique; Ghoorah, Anisah; Torchala, Mieczyslaw; Chaleil, Raphael 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, Francoise; Guerois, Raphael; Vangone, Anna; Rodrigues, Joao 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; Jimenez-Garcia, Brian; Moal, Iain H.; Fernandez-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; Burman, Shourya S. Roy; Gray, Jeffrey J.; Chermak, Edrisse; Cavallo, Luigi; Oliva, Romina; Tovchigrechko, Andrey; Wodak, Shoshana J. 分享 收藏
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