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Your search keyword '"Yang, Jinsol"' showing total 8 results
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8 results on '"Yang, Jinsol"'

3. Discovery of Highly Active Kynureninases for Cancer Immunotherapy through Protein Language Model

Author

Eom, Hyunuk, primary, Cho, Kye Soo, additional, Lee, Jihyeon, additional, Kim, Stephanie, additional, Park, Sukhwan, additional, Kim, Hyunbin, additional, Yang, Jinsol, additional, Han, Young-Hyun, additional, Lee, Juyong, additional, Seok, Chaok, additional, Lee, Myeong Sup, additional, Song, Woon Ju, additional, and Steinegger, Martin, additional

Published
2024
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5. GalaxyDock2‐HEME: Protein–ligand docking for heme proteins.

Author

Lee, Changsoo, Yang, Jinsol, Kwon, Sohee, and Seok, Chaok

Subjects
*HEMOPROTEINS, *MOLECULAR docking, *LIGAND binding (Biochemistry), *SIGNAL recognition particle receptor, *COMPUTER-assisted drug design, *COORDINATION polymers, *IRON, *PROTEIN-ligand interactions
Abstract

Prediction of protein–ligand binding poses is an essential component for understanding protein–ligand interactions and computer‐aided drug design. Various proteins involve prosthetic groups such as heme for their functions, and adequate consideration of the prosthetic groups is vital for protein–ligand docking. Here, we extend the GalaxyDock2 protein–ligand docking algorithm to handle ligand docking to heme proteins. Docking to heme proteins involves increased complexity because the interaction of heme iron and ligand has covalent nature. GalaxyDock2‐HEME, a new protein–ligand docking program for heme proteins, has been developed based on GalaxyDock2 by adding an orientation‐dependent scoring term to describe heme iron‐ligand coordination interaction. This new docking program performs better than other noncommercial docking programs such as EADock with MMBP, AutoDock Vina, PLANTS, LeDock, and GalaxyDock2 on a heme protein–ligand docking benchmark set in which ligands are known to bind iron. In addition, docking results on two other sets of heme protein–ligand complexes in which ligands do not bind iron show that GalaxyDock2‐HEME does not have a high bias toward iron binding compared to other docking programs. This implies that the new docking program can distinguish iron binders from noniron binders for heme proteins. [ABSTRACT FROM AUTHOR]

Published
2023
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7. Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment

Author

Lensink, Marc F., primary, Brysbaert, Guillaume, additional, Mauri, Théo, additional, Nadzirin, Nurul, additional, Velankar, Sameer, additional, Chaleil, Raphael A. G., additional, Clarence, Tereza, additional, Bates, Paul A., additional, Kong, Ren, additional, Liu, Bin, additional, Yang, Guangbo, additional, Liu, Ming, additional, Shi, Hang, additional, Lu, Xufeng, additional, Chang, Shan, additional, Roy, Raj S., additional, Quadir, Farhan, additional, Liu, Jian, additional, Cheng, Jianlin, additional, Antoniak, Anna, additional, Czaplewski, Cezary, additional, Giełdoń, Artur, additional, Kogut, Mateusz, additional, Lipska, Agnieszka G., additional, Liwo, Adam, additional, Lubecka, Emilia A., additional, Maszota‐Zieleniak, Martyna, additional, Sieradzan, Adam K., additional, Ślusarz, Rafał, additional, Wesołowski, Patryk A., additional, Zięba, Karolina, additional, Del Carpio Muñoz, Carlos A., additional, Ichiishi, Eiichiro, additional, Harmalkar, Ameya, additional, Gray, Jeffrey J., additional, Bonvin, Alexandre M. J. J., additional, Ambrosetti, Francesco, additional, Vargas Honorato, Rodrigo, additional, Jandova, Zuzana, additional, Jiménez‐García, Brian, additional, Koukos, Panagiotis I., additional, Van Keulen, Siri, additional, Van Noort, Charlotte W., additional, Réau, Manon, additional, Roel‐Touris, Jorge, additional, Kotelnikov, Sergei, additional, Padhorny, Dzmitry, additional, Porter, Kathryn A., additional, Alekseenko, Andrey, additional, Ignatov, Mikhail, additional, Desta, Israel, additional, Ashizawa, Ryota, additional, Sun, Zhuyezi, additional, Ghani, Usman, additional, Hashemi, Nasser, additional, Vajda, Sandor, additional, Kozakov, Dima, additional, Rosell, Mireia, additional, Rodríguez‐Lumbreras, Luis A., additional, Fernandez‐Recio, Juan, additional, Karczynska, Agnieszka, additional, Grudinin, Sergei, additional, Yan, Yumeng, additional, Li, Hao, additional, Lin, Peicong, additional, Huang, Sheng‐You, additional, Christoffer, Charles, additional, Terashi, Genki, additional, Verburgt, Jacob, additional, Sarkar, Daipayan, additional, Aderinwale, Tunde, additional, Wang, Xiao, additional, Kihara, Daisuke, additional, Nakamura, Tsukasa, additional, Hanazono, Yuya, additional, Gowthaman, Ragul, additional, Guest, Johnathan D., additional, Yin, Rui, additional, Taherzadeh, Ghazaleh, additional, Pierce, Brian G., additional, Barradas‐Bautista, Didier, additional, Cao, Zhen, additional, Cavallo, Luigi, additional, Oliva, Romina, additional, Sun, Yuanfei, additional, Zhu, Shaowen, additional, Shen, Yang, additional, Park, Taeyong, additional, Woo, Hyeonuk, additional, Yang, Jinsol, additional, Kwon, Sohee, additional, Won, Jonghun, additional, Seok, Chaok, additional, Kiyota, Yasuomi, additional, Kobayashi, Shinpei, additional, Harada, Yoshiki, additional, Takeda‐Shitaka, Mayuko, additional, Kundrotas, Petras J., additional, Singh, Amar, additional, Vakser, Ilya A., additional, Dapkūnas, Justas, additional, Olechnovič, Kliment, additional, Venclovas, Česlovas, additional, Duan, Rui, additional, Qiu, Liming, additional, Xu, Xianjin, additional, Zhang, Shuang, additional, Zou, Xiaoqin, additional, and Wodak, Shoshana J., additional

Published
2021
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8. Protein oligomer structure prediction using GALAXY in CASP14.

Author

Park, Taeyong, Woo, Hyeonuk, Yang, Jinsol, Kwon, Sohee, Won, Jonghun, and Seok, Chaok

Abstract

Proteins perform their functions by interacting with other biomolecules. For these interactions, proteins often form homo‐ or hetero‐oligomers as well. Thus, oligomer protein structures provide important clues regarding the biological roles of proteins. To this end, computational prediction of oligomer structures may be a useful tool in the absence of experimentally resolved structures. Here, we describe our server and human‐expert methods used to predict oligomer structures in the CASP14 experiment. Examples are provided for cases in which manual domain‐splitting led to improved oligomeric domain structures by ab initio docking, automated oligomer structure refinement led to improved subunit orientation and terminal structure, and manual oligomer modeling utilizing literature information generated a reasonable oligomer model. We also discussed the results of post‐prediction docking calculations with AlphaFold2 monomers as input in comparison to our blind prediction results. Overall, ab initio docking of AlphaFold2 models did not lead to better oligomer structure prediction, which may be attributed to the interfacial structural difference between the AlphaFold2 monomer structures and the crystal oligomer structures. This result poses a next‐stage challenge in oligomer structure prediction after the success of AlphaFold2. For successful protein assembly structure prediction, a different approach that exploits further evolutionary information on the interface and/or flexible docking taking the interfacial conformational flexibilities of subunit structures into account is needed. [ABSTRACT FROM AUTHOR]

Published
2021
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