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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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7. 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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9. 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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11. Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment

Author

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

Published
2021

12. Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment

Author

Cancer Research UK, Department of Energy and Climate Change (UK), European Commission, Institut National de Recherche en Informatique et en Automatique (France), Medical Research Council (UK), Japan Society for the Promotion of Science, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), National Institute of General Medical Sciences (US), National Institutes of Health (US), National Natural Science Foundation of China, National Science Foundation (US), Lensink, Marc F., Brysbaert, Guillaume, Mauri, Théo, Nadzirin, Nurul, Velankar, Sameer, Chaleil, Raphaël A. G., Clarence, Tereza, Bates, Paul A., Kong, Ren, Liu, Bin, Yang, Guangbo, Liu, Ming, Shi, Hang, Lu, Xufeng, Chang, Xang, Roy, Raj S., Quadir, Farhan, Liu, Jian, Cheng, Jianlin, Antoniak, Anna, Czaplewski, Cezary, Giełdón, Artur, Kogut, Mateusz, Lipska, Agnieszka, Liwo, Adam, Lubecka, Emilia, Maszota-Zieleniak, Martyna, Sieradzan, Adam K., Ślusarz, Rafał, Wesołowski, Patryk A., Zięba, Karolina, Carpio Muñoz, Carlos A. del, Ichiishi, Eiichiro, Harmalkar, Ameya, Gray, Jeffrey J., Bonvin, Alexandre M. J. J., Ambrosetti, Francesco, Vargas Honorato, Rodrigo, Jandova, Zuzana, Jiménez-García, Brian, Koukos, Panagiotis I., Keulen, Siri van, Noort, Charlotte W. van, Réau, Manon, Roel-Touris, Jorge, Kotelnikov, Sergey, Padhorny, Dzmitry, Porter, Kathryn, Alekseenko, Andrey, Ignatov, Mikhail, Desta, Israel, Ashizawa, Ryota, Sun, Zhuyezi, Ghani, Usman, Hashemi, Nasser, Vajda, Sandor, Kozakov, Dima, Rosell, Mireia, Rodríguez-Lumbreras, Luis A., Fernández-Recio, Juan, Karczynska, Agnieszka, Grudinin, Sergei, Yan, Yumeng, Li, Hao, Lin, Peicong, Huang, Sheng-You, Christoffer, Charles, Terashi, Genki, Verburgt, Jacob, Sarkar, Daipayan, Aderinwale, Tunde, Wang, Xiao, Kihara, Daisuke, Nakamura, Tsukasa, Hanazono, Huya, Gowthaman, Ragul, Guest, Johnathan D., Yin, Rui, Taherzadeh, Ghazaleh, Pierce, Brian G., Barradas-Bautista, Didier, Cao, Zhen, Cavallo, Luigi, Oliva, Romina, Sun, Yuanfei, Zhu, Shaowen, Shen, Yang, Park, Taeyong, Woo, Hyeonuk, Yang, Jinsol, Kwon, Sohee, Won, Jonghun, Seok, Chaok, Kiyota, Yasuomi, Kobayashi, Shinpei, Harada, Yoshiki, Takeda-Shitaka, Mayuko, Kundrotas, Petras J., Singh, Amar, Vakser, Ilya A., Dapkunas, Justas, Olechnovic, Kliment, Venclovas, Česlovas, Duan, Rui, Qiu, Liming, Xu, Xianjin, Zhang, Shuang, Zou, Xiaoqin, Wodak, Shoshana J., Cancer Research UK, Department of Energy and Climate Change (UK), European Commission, Institut National de Recherche en Informatique et en Automatique (France), Medical Research Council (UK), Japan Society for the Promotion of Science, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), National Institute of General Medical Sciences (US), National Institutes of Health (US), National Natural Science Foundation of China, National Science Foundation (US), Lensink, Marc F., Brysbaert, Guillaume, Mauri, Théo, Nadzirin, Nurul, Velankar, Sameer, Chaleil, Raphaël A. G., Clarence, Tereza, Bates, Paul A., Kong, Ren, Liu, Bin, Yang, Guangbo, Liu, Ming, Shi, Hang, Lu, Xufeng, Chang, Xang, Roy, Raj S., Quadir, Farhan, Liu, Jian, Cheng, Jianlin, Antoniak, Anna, Czaplewski, Cezary, Giełdón, Artur, Kogut, Mateusz, Lipska, Agnieszka, Liwo, Adam, Lubecka, Emilia, Maszota-Zieleniak, Martyna, Sieradzan, Adam K., Ślusarz, Rafał, Wesołowski, Patryk A., Zięba, Karolina, Carpio Muñoz, Carlos A. del, Ichiishi, Eiichiro, Harmalkar, Ameya, Gray, Jeffrey J., Bonvin, Alexandre M. J. J., Ambrosetti, Francesco, Vargas Honorato, Rodrigo, Jandova, Zuzana, Jiménez-García, Brian, Koukos, Panagiotis I., Keulen, Siri van, Noort, Charlotte W. van, Réau, Manon, Roel-Touris, Jorge, Kotelnikov, Sergey, Padhorny, Dzmitry, Porter, Kathryn, Alekseenko, Andrey, Ignatov, Mikhail, Desta, Israel, Ashizawa, Ryota, Sun, Zhuyezi, Ghani, Usman, Hashemi, Nasser, Vajda, Sandor, Kozakov, Dima, Rosell, Mireia, Rodríguez-Lumbreras, Luis A., Fernández-Recio, Juan, Karczynska, Agnieszka, Grudinin, Sergei, Yan, Yumeng, Li, Hao, Lin, Peicong, Huang, Sheng-You, Christoffer, Charles, Terashi, Genki, Verburgt, Jacob, Sarkar, Daipayan, Aderinwale, Tunde, Wang, Xiao, Kihara, Daisuke, Nakamura, Tsukasa, Hanazono, Huya, Gowthaman, Ragul, Guest, Johnathan D., Yin, Rui, Taherzadeh, Ghazaleh, Pierce, Brian G., Barradas-Bautista, Didier, Cao, Zhen, Cavallo, Luigi, Oliva, Romina, Sun, Yuanfei, Zhu, Shaowen, Shen, Yang, Park, Taeyong, Woo, Hyeonuk, Yang, Jinsol, Kwon, Sohee, Won, Jonghun, Seok, Chaok, Kiyota, Yasuomi, Kobayashi, Shinpei, Harada, Yoshiki, Takeda-Shitaka, Mayuko, Kundrotas, Petras J., Singh, Amar, Vakser, Ilya A., Dapkunas, Justas, Olechnovic, Kliment, Venclovas, Česlovas, Duan, Rui, Qiu, Liming, Xu, Xianjin, Zhang, Shuang, Zou, Xiaoqin, and Wodak, Shoshana J.

Abstract

We present the results for CAPRI Round 50, the fourth joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and three higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly related templates were found for the individual subunits. Twenty-five CAPRI groups including eight automatic servers submitted ~1250 models per target. Twenty groups including six servers participated in the CAPRI scoring challenge submitted ~190 models per target. The accuracy of the predicted models was evaluated using the classical CAPRI criteria. The prediction performance was measured by a weighted scoring scheme that takes into account the number of models of acceptable quality or higher submitted by each group as part of their five top-ranking models. Compared to the previous CASP-CAPRI challenge, top performing groups submitted such models for a larger fraction (70–75%) of the targets in this Round, but fewer of these models were of high accuracy. Scorer groups achieved stronger performance with more groups submitting correct models for 70–80% of the targets or achieving high accuracy predictions. Servers performed less well in general, except for the MDOCKPP and LZERD servers, who performed on par with human groups. In addition to these results, major advances in methodology are discussed, providing an informative overview of where the prediction of protein assemblies currently stands.

Published
2021

17. Structure prediction of biological assemblies using GALAXY in CAPRI rounds 38‐45.

Author

Park, Taeyong, Woo, Hyeonuk, Baek, Minkyung, Yang, Jinsol, and Seok, Chaok

Abstract

We participated in CARPI rounds 38‐45 both as a server predictor and a human predictor. These CAPRI rounds provided excellent opportunities for testing prediction methods for three classes of protein interactions, that is, protein‐protein, protein‐peptide, and protein‐oligosaccharide interactions. Both template‐based methods (GalaxyTBM for monomer protein, GalaxyHomomer for homo‐oligomer protein, GalaxyPepDock for protein‐peptide complex) and ab initio docking methods (GalaxyTongDock and GalaxyPPDock for protein oligomer, GalaxyPepDock‐ab‐initio for protein‐peptide complex, GalaxyDock2 and Galaxy7TM for protein‐oligosaccharide complex) have been tested. Template‐based methods depend heavily on the availability of proper templates and template‐target similarity, and template‐target difference is responsible for inaccuracy of template‐based models. Inaccurate template‐based models could be improved by our structure refinement and loop modeling methods based on physics‐based energy optimization (GalaxyRefineComplex and GalaxyLoop) for several CAPRI targets. Current ab initio docking methods require accurate protein structures as input. Small conformational changes from input structure could be accounted for by our docking methods, producing one of the best models for several CAPRI targets. However, predicting large conformational changes involving protein backbone is still challenging, and full exploration of physics‐based methods for such problems is still to come. [ABSTRACT FROM AUTHOR]

Published
2020
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