Chaok Seok

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 41

Top Topics

Molecular Dynamics Simulations

Structural Basis

Top Venues

Nature communications

Journal of chemical information and modeling

PLoS computational biology

This page only lists publications with an associated author ORCID identifier.

Publications

Changsoo Lee, Jonghun Won, Seongok Ryu, Jinsol Yang, Nuri Jung, Hahnbeom Park, Chaok Seok
GalaxyDock-DL: Protein-Ligand Docking by Global Optimization and Neural Network Energy. Journal of chemical theory and computation (2024)
Hyeonuk Woo, Yubeen Kim, Chaok Seok
Protein loop structure prediction by community-based deep learning and its application to antibody CDR H3 loop modeling. PLoS computational biology 20 (6) (2024)
Hyeonuk Woo, Yubeen Kim, Chaok Seok
Protein loop structure prediction by community-based deep learning and its application to antibody CDR H3 loop modeling. PLoS computational biology 20 (6) (2024)
Hyeonuk Woo, Yubeen Kim, Chaok Seok
Protein loop structure prediction by community-based deep learning and its application to antibody CDR H3 loop modeling. PLoS computational biology 20 (6) (2024)
Hyeonuk Woo, Yubeen Kim, Chaok Seok
Protein loop structure prediction by community-based deep learning and its application to antibody CDR H3 loop modeling. PLoS computational biology 20 (6) (2024)
Seho Lee, Chaok Seok, Hahnbeom Park
Benchmarking applicability of medium-resolution cryo-EM protein structures for structure-based drug design. Journal of computational chemistry (2023)
Changsoo Lee, Jinsol Yang, Sohee Kwon, Chaok Seok
GalaxyDock2-HEME: Protein-ligand docking for heme proteins. Journal of computational chemistry (2023)
Chulwon Choi, Jungnam Bae, Seonghan Kim, Seho Lee, Hyunook Kang, Jinuk Kim, Injin Bang, Kiheon Kim, Won-Ki Huh, Chaok Seok, Hahnbeom Park, Wonpil Im, Hee-Jung Choi
Understanding the molecular mechanisms of odorant binding and activation of the human OR52 family. Nature communications 14 (1) (2023)
Jihyeon Lee, Chaok Seok, Sihyun Ham, Song-Ho Chong
Atomic-level thermodynamics analysis of the binding free energy of SARS-CoV-2 neutralizing antibodies. Proteins (2022)
Jihyeon Lee, Chaok Seok, Sihyun Ham, Song-Ho Chong
Atomic-Level Thermodynamics Analysis of the Binding Free Energy of SARS-CoV-2 Neutralizing Antibodies. Proteins (2022)
Chaehee Park, Jinuk Kim, Seung-Bum Ko, Yeol Kyo Choi, Hyeongseop Jeong, Hyeonuk Woo, Hyunook Kang, Injin Bang, Sang Ah Kim, Tae-Young Yoon, Chaok Seok, Wonpil Im, Hee-Jung Choi
Structural basis of neuropeptide Y signaling through Y1 receptor. Nature communications 13 (1) (2022)
Sangwoo Park, Chaok Seok
GalaxyWater-CNN: Prediction of Water Positions on the Protein Structure by a 3D-Convolutional Neural Network. Journal of chemical information and modeling 62 (13) (2022)
Jihyeon Lee, Chaok Seok, Sihyun Ham, Song-Ho Chong
Atomic-level thermodynamics analysis of the binding free energy of SARS-CoV-2 neutralizing antibodies. Proteins (2022)
Jiho Sim, Sohee Kwon, Chaok Seok
HProteome-BSite: predicted binding sites and ligands in human 3D proteome. Nucleic acids research (2022)
Jihyeon Lee, Chaok Seok, Sihyun Ham, Song-Ho Chong
Atomic-level thermodynamics analysis of the binding free energy of SARS-CoV-2 neutralizing antibodies. Proteins (2022)
Chaehee Park, Jinuk Kim, Seung-Bum Ko, Yeol Kyo Choi, Hyeongseop Jeong, Hyeonuk Woo, Hyunook Kang, Injin Bang, Sang Ah Kim, Tae-Young Yoon, Chaok Seok, Wonpil Im, Hee-Jung Choi
Author Correction: Structural basis of neuropeptide Y signaling through Y1 receptor. Nature communications 13 (1) (2022)
Jinuk Kim, Wonhee Han, Taeyong Park, Eun Jin Kim, Injin Bang, Hyun Sik Lee, Yejin Jeong, Kyeonghwan Roh, Jeesoo Kim, Jong-Seo Kim, Chanhee Kang, Chaok Seok, Jin-Kwan Han, Hee-Jung Choi
Author Correction: Sclerostin inhibits Wnt signaling through tandem interaction with two LRP6 ectodomains. Nature communications 13 (1) (2022)
Yiwei Cao, Yeol Kyo Choi, Martin Frank, Hyeonuk Woo, Sang-Jun Park, Min Sun Yeom, Chaok Seok, Wonpil Im
Dynamic Interactions of Fully Glycosylated SARS-CoV-2 Spike Protein with Various Antibodies. Journal of chemical theory and computation 17 (10) (2021)
Lim Heo, Sangwoo Park, Chaok Seok
GalaxyWater-wKGB: Prediction of Water Positions on Protein Structure Using wKGB Statistical Potential. Journal of chemical information and modeling 61 (5) (2021)
Andriy Kryshtafovych, John Moult, Wendy M Billings, Dennis Della Corte, Krzysztof Fidelis, Sohee Kwon, Kliment Olechnovič, Chaok Seok, Česlovas Venclovas, Jonghun Won, null null
Modeling SARS-CoV-2 proteins in the CASP-commons experiment. Proteins 89 (12) (2021)
Taeyong Park, Hyeonuk Woo, Jinsol Yang, Sohee Kwon, Jonghun Won, Chaok Seok
Protein oligomer structure prediction using GALAXY in CASP14. Proteins 89 (12) (2021)
Yeol Kyo Choi, Yiwei Cao, Martin Frank, Hyeonuk Woo, Sang-Jun Park, Min Sun Yeom, Tristan I Croll, Chaok Seok, Wonpil Im
Structure, Dynamics, Receptor Binding, and Antibody Binding of the Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein in a Viral Membrane. Journal of chemical theory and computation 17 (4) (2021)
Sohee Kwon, Jonghun Won, Andriy Kryshtafovych, Chaok Seok
Assessment of protein model structure accuracy estimation in CASP14: Old and new challenges. Proteins 89 (12) (2021)
Taeyong Park, Jonghun Won, Minkyung Baek, Chaok Seok
GalaxyHeteromer: protein heterodimer structure prediction by template-based and ab initio docking. Nucleic acids research 49 (W1) (2021)
Marc F Lensink, Guillaume Brysbaert, Théo Mauri, Nurul Nadzirin, Sameer Velankar, Raphael A G Chaleil, Tereza Clarence, Paul A Bates, Ren Kong, Bin Liu, Guangbo Yang, Ming Liu, Hang Shi, Xufeng Lu, Shan Chang, Raj S Roy, Farhan Quadir, Jian Liu, Jianlin Cheng, Anna Antoniak, Cezary Czaplewski, Artur Giełdoń, Mateusz Kogut, Agnieszka G Lipska, Adam Liwo, Emilia A Lubecka, Martyna Maszota-Zieleniak, Adam K Sieradzan, Rafał Ślusarz, Patryk A Wesołowski, Karolina Zięba, Carlos A Del Carpio Muñoz, Eiichiro Ichiishi, Ameya Harmalkar, Jeffrey J Gray, Alexandre M J J Bonvin, Francesco Ambrosetti, Rodrigo Vargas Honorato, Zuzana Jandova, Brian Jiménez-García, Panagiotis I Koukos, Siri Van Keulen, Charlotte W Van Noort, Manon Réau, Jorge Roel-Touris, Sergei Kotelnikov, Dzmitry Padhorny, Kathryn A Porter, Andrey Alekseenko, Mikhail Ignatov, Israel Desta, Ryota Ashizawa, Zhuyezi Sun, Usman Ghani, Nasser Hashemi, Sandor Vajda, Dima Kozakov, Mireia Rosell, Luis A Rodríguez-Lumbreras, Juan Fernández-Recio, Agnieszka Karczynska, Sergei Grudinin, Yumeng Yan, Hao Li, Peicong Lin, Sheng-You Huang, Charles W Christoffer, Genki Terashi, Jacob Verburgt, Daipayan Sarkar, Tunde Aderinwale, Xiao Wang, Daisuke Kihara, Tsukasa Nakamura, Yuya Hanazono, Ragul Gowthaman, Johnathan D Guest, Rui Yin, Ghazaleh Taherzadeh, Brian G Pierce, Didier Barradas-Bautista, Zhen Cao, Luigi Cavallo, Romina Oliva, Yuanfei Sun, Shaowen Zhu, Yang Shen, Taeyong Park, Hyeonuk Woo, Jinsol Yang, Sohee Kwon, Jonghun Won, Chaok Seok, Yasuomi Kiyota, Shinpei Kobayashi, Yoshiki Harada, Mayuko Takeda-Shitaka, Petras J Kundrotas, Amar Singh, Ilya A Vakser, Justas Dapkunas, Kliment Olechnovič, Česlovas Venclovas, Rui Duan, Liming Qiu, Xianjin Xu, Shuang Zhang, Xiaoqin Zou, Shoshana J Wodak
Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment. Proteins 89 (12) (2021)
Beomchang Kang, Chaok Seok, Juyong Lee
MOLGENGO: Finding Novel Molecules with Desired Electronic Properties by Capitalizing on Their Global Optimization. ACS omega 6 (41) (2021)
Jinuk Kim, Wonhee Han, Taeyong Park, Eun Jin Kim, Injin Bang, Hyun Sik Lee, Yejing Jeong, Kyeonghwan Roh, Jeesoo Kim, Jong-Seo Kim, Chanhee Kang, Chaok Seok, Jin-Kwan Han, Hee-Jung Choi
Sclerostin inhibits Wnt signaling through tandem interaction with two LRP6 ectodomains. Nature communications 11 (1) (2020)
Beomchang Kang, Chaok Seok, Juyong Lee
Prediction of Molecular Electronic Transitions Using Random Forests. Journal of chemical information and modeling 60 (12) (2020)
Hyeonuk Woo, Sang-Jun Park, Yeol Kyo Choi, Taeyong Park, Maham Tanveer, Yiwei Cao, Nathan R Kern, Jumin Lee, Min Sun Yeom, Tristan I Croll, Chaok Seok, Wonpil Im
Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane. The journal of physical chemistry. B 124 (33) (2020)
Jinsol Yang, Sohee Kwon, Sang-Hun Bae, Kyoung Mii Park, Changsik Yoon, Ji-Hyun Lee, Chaok Seok
GalaxySagittarius: Structure- and Similarity-Based Prediction of Protein Targets for Druglike Compounds. Journal of chemical information and modeling 60 (6) (2020)
Taeyong Park, Minkyung Baek, Hasup Lee, Chaok Seok
GalaxyTongDock: Symmetric and asymmetric ab initio protein-protein docking web server with improved energy parameters. Journal of computational chemistry 40 (27) (2019)
Taeyong Park, Hyeonuk Woo, Minkyung Baek, Jinsol Yang, Chaok Seok
Structure prediction of biological assemblies using GALAXY in CAPRI rounds 38-45. Proteins 88 (8) (2019)
Jinsol Yang, Minkyung Baek, Chaok Seok
GalaxyDock3: Protein-ligand docking that considers the full ligand conformational flexibility. Journal of computational chemistry 40 (31) (2019)
Marc F Lensink, Guillaume Brysbaert, Nurul Nadzirin, Sameer Velankar, Raphael A G Chaleil, Tereza Gerguri, Paul A Bates, Elodie Laine, Alessandra Carbone, Sergei Grudinin, Ren Kong, Ran-Ran Liu, Xi-Ming Xu, Hang Shi, Shan Chang, Miriam Eisenstein, Agnieszka Karczynska, Cezary Czaplewski, Emilia Lubecka, Agnieszka Lipska, Paweł Krupa, Magdalena Mozolewska, Łukasz Golon, Sergey Samsonov, Adam Liwo, Silvia Crivelli, Guillaume Pagès, Mikhail Karasikov, Maria Kadukova, Yumeng Yan, Sheng-You Huang, Mireia Rosell, Luis A Rodríguez-Lumbreras, Miguel Romero-Durana, Lucía Díaz-Bueno, Juan Fernández-Recio, Charles W Christoffer, Genki Terashi, Woong-Hee Shin, Tunde Aderinwale, Sai Raghavendra Maddhuri Venkata Subraman, Daisuke Kihara, Dima Kozakov, Sandor Vajda, Kathryn Porter, Dzmitry Padhorny, Israel Desta, Dmitri Beglov, Mikhail Ignatov, Sergey Kotelnikov, Iain H Moal, David W Ritchie, Isaure Chauvot de Beauchene, Bernard Maigret, Marie-Dominique Devignes, Maria E Ruiz Echartea, Didier Barradas-Bautista, Zhen Cao, Luigi Cavallo, Romina Oliva, Yue Cao, Yang Shen, Minkyung Baek, Taeyong Park, Hyeonuk Woo, Chaok Seok, Merav Braitbard, Lirane Bitton, Dina Scheidman-Duhovny, Justas Dapkunas, Kliment Olechnovič, Česlovas Venclovas, Petras J Kundrotas, Saveliy Belkin, Devlina Chakravarty, Varsha D Badal, Ilya A Vakser, Thom Vreven, Sweta Vangaveti, Tyler Borrman, Nishigandha Phalke, Johnathan D Guest, Ragul Gowthaman, Brian G Pierce, Xianjin Xu, Rui Duan, Liming Qiu, Jie Hou, Benjamin Ryan Merideth, Zhiwei Ma, Jianlin Cheng, Xiaoqin Zou, Panagiotis I Koukos, Jorge Roel-Touris, Francesco Ambrosetti, Cunliang Geng, Jörg Schaarschmidt, Mikael E Trellet, Adrien S J Melquiond, Li Xue, Brian Jiménez-García, Charlotte W van Noort, Rodrigo V Honorato, Alexandre M J J Bonvin, Shoshana J Wodak
Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment. Proteins 87 (12) (2019)
Jonghun Won, Minkyung Baek, Bohdan Monastyrskyy, Andriy Kryshtafovych, Chaok Seok
Assessment of protein model structure accuracy estimation in CASP13: Challenges in the era of deep learning. Proteins 87 (12) (2019)
Minkyung Baek, Taeyong Park, Hyeonuk Woo, Chaok Seok
Prediction of protein oligomer structures using GALAXY in CASP13. Proteins 87 (12) (2019)
Jonghun Won, Gyu Rie Lee, Hahnbeom Park, Chaok Seok
GalaxyGPCRloop: Template-Based and Ab Initio Structure Sampling of the Extracellular Loops of G-Protein-Coupled Receptors. Journal of chemical information and modeling 58 (6) (2018)
Gyu Rie Lee, Lim Heo, Chaok Seok
Simultaneous refinement of inaccurate local regions and overall structure in the CASP12 protein model refinement experiment. Proteins (2017)
Xiangqiang Shao, Hyunook Kang, Timothy Loveless, Gyu Rie Lee, Chaok Seok, William I Weis, Hee-Jung Choi, Jeff Hardin
Cell-cell adhesion in metazoans relies on evolutionarily conserved features of the α-catenin·β-catenin-binding interface. The Journal of biological chemistry 292 (40) (2017)
Minkyung Baek, Woong-Hee Shin, Hwan Won Chung, Chaok Seok
GalaxyDock BP2 score: a hybrid scoring function for accurate protein-ligand docking. Journal of computer-aided molecular design 31 (7) (2017)
Marc F Lensink, Sameer Velankar, Minkyung Baek, Lim Heo, Chaok Seok, Shoshana J Wodak
The challenge of modeling protein assemblies: the CASP12-CAPRI experiment. Proteins (2017)