J
Jong Yun Kim
Researcher at Korea Institute for Advanced Study
Publications - 6
Citations - 214
Jong Yun Kim is an academic researcher from Korea Institute for Advanced Study. The author has contributed to research in topics: Protein structure prediction & Global optimization. The author has an hindex of 5, co-authored 6 publications receiving 185 citations. Previous affiliations of Jong Yun Kim include Protein Sciences.
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Journal ArticleDOI
Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.
Marc F. Lensink,Sameer Velankar,Andriy Kryshtafovych,Shen You Huang,Dina Schneidman-Duhovny,Andrej Sali,Joan Segura,Narcis Fernandez-Fuentes,Shruthi Viswanath,Ron Elber,Sergei Grudinin,Petr Popov,Emilie Neveu,Hasup Lee,Minkyung Baek,Sangwoo Park,Lim Heo,Gyu Rie Lee,Chaok Seok,Sanbo Qin,Huan-Xiang Zhou,David W. Ritchie,Bernard Maigret,Marie-Dominique Devignes,Anisah W. Ghoorah,Mieczyslaw Torchala,Raphael A. G. Chaleil,Paul A. Bates,Efrat Ben-Zeev,Miriam Eisenstein,Surendra S. Negi,Zhiping Weng,Thom Vreven,Brian G. Pierce,Tyler M. Borrman,Jinchao Yu,Françoise Ochsenbein,Raphael Guerois,Anna Vangone,João P. G. L. M. Rodrigues,Gydo C. P. van Zundert,Mehdi Nellen,Li C. Xue,Ezgi Karaca,Adrien S. J. Melquiond,Koen M. Visscher,Panagiotis L. Kastritis,Alexandre M. J. J. Bonvin,Xianjin Xu,Liming Qiu,Chengfei Yan,Jilong Li,Zhiwei Ma,Jianlin Cheng,Xiaoqin Zou,Yang Shen,Lenna X. Peterson,Hyung Rae Kim,Amit Roy,Amit Roy,Xusi Han,Juan Esquivel-Rodríguez,Daisuke Kihara,Xiaofeng Yu,Neil J. Bruce,Jonathan C. Fuller,Rebecca C. Wade,Ivan Anishchenko,Petras J. Kundrotas,Ilya A. Vakser,Kenichiro Imai,Kazunori D. Yamada,Toshiyuki Oda,Tsukasa Nakamura,Kentaro Tomii,Chiara Pallara,Miguel Romero-Durana,Brian Jiménez-García,Iain H. Moal,Juan Fernández-Recio,Jong Young Joung,Jong Yun Kim,Keehyoung Joo,Jooyoung Lee,Jooyoung Lee,Dima Kozakov,Sandor Vajda,Scott E. Mottarella,David R. Hall,Dmitri Beglov,Artem B. Mamonov,Bing Xia,Tanggis Bohnuud,Carlos A. Del Carpio,Carlos A. Del Carpio,Eichiro Ichiishi,Nicholas A. Marze,Daisuke Kuroda,Shourya S. Roy Burman,Jeffrey J. Gray,Edrisse Chermak,Luigi Cavallo,Romina Oliva,Andrey Tovchigrechko,Shoshana J. Wodak +104 more
TL;DR: Results show that the prediction of homodimer assemblies by homology modeling techniques and docking calculations is quite successful for targets featuring large enough subunit interfaces to represent stable associations, and that docking procedures tend to perform better than standard homology modeled techniques.
Journal ArticleDOI
Template based protein structure modeling by global optimization in CASP11.
Keehyoung Joo,InSuk Joung,Sun Young Lee,Jong Yun Kim,Qianyi Cheng,Balachandran Manavalan,Jong Young Joung,Seungryong Heo,Juyong Lee,Mikyung Nam,In-Ho Lee,In-Ho Lee,Sung Jong Lee,Sung Jong Lee,Jooyoung Lee +14 more
TL;DR: The improved performance of the nns server method is attributed to successful fold recognition achieved by combining several methods including CRFalign and to the current modeling formulation that can incorporate native‐like structural aspects present in multiple templates.
Journal ArticleDOI
Protein structure modeling and refinement by global optimization in CASP12.
Seung Hwan Hong,InSuk Joung,Jose C. Flores-Canales,Balachandran Manavalan,Qianyi Cheng,Seungryong Heo,Jong Yun Kim,Sun Young Lee,Mikyung Nam,Keehyoung Joo,In-Ho Lee,Sung Jong Lee,Jooyoung Lee +12 more
TL;DR: For protein structure modeling in the CASP12 experiment, a new protocol based on the previous CASP11 approach is developed, where the template term played a less significant role than it did in LEE, complemented by increased contributions from other terms such as the predicted contact term.
Journal ArticleDOI
Conformational Space Annealing explained: A general optimization algorithm, with diverse applications
TL;DR: The performance of CSA is shown to be better than or similar to the most popular optimization method, simulated annealing, and the way PyCSA can be applied to a discrete objective function, namely a parameter optimization problem is demonstrated.
Journal ArticleDOI
Template‐free modeling by LEE and LEER in CASP11
InSuk Joung,Sun Young Lee,Qianyi Cheng,Qianyi Cheng,Jong Yun Kim,Keehyoung Joo,Sung Jong Lee,Jooyoung Lee,Jooyoung Lee +8 more
TL;DR: CASP11 results indicate that LEE models were better than the average template models in terms of both backbone structures and side‐chain orientations, and LEER models were of improved physical realism and stereo‐chemistry compared to LEE model, and they were comparable to L EE models in the backbone accuracy.