The diversity of H3 loops determines the antigen‐binding tendencies of antibody CDR loops

por Tsuchiya, Yuko, Mizuguchi, Kenji
Publicado en Protein Sci (2016)

Neural networks for protein structure and function prediction and dynamic analysis

por Tsuchiya, Yuko, Tomii, Kentaro
Publicado en Biophys Rev (2020)

Discrimination between biological interfaces and crystal-packing contacts

por Tsuchiya, Yuko, Nakamura, Haruki, Kinoshita, Kengo
Publicado 2008

PreBI: prediction of biological interfaces of proteins in crystals

por Tsuchiya, Yuko, Kinoshita, Kengo, Ito, Nobutoshi, Nakamura, Haruki
Publicado 2006

Classification of heterodimer interfaces using docking models and construction of scoring functions for the complex structure prediction

por Tsuchiya, Yuko, Kanamori, Eiji, Nakamura, Haruki, Kinoshita, Kengo
Publicado 2009

Dynamic features of homodimer interfaces calculated by normal-mode analysis

por Tsuchiya, Yuko, Kinoshita, Kengo, Endo, Shigeru, Wako, Hiroshi
Publicado 2012

A study of CDR3 loop dynamics reveals distinct mechanisms of peptide recognition by T‐cell receptors exhibiting different levels of cross‐reactivity

por Tsuchiya, Yuko, Namiuchi, Yoshiki, Wako, Hiroshi, Tsurui, Hiromichi
Publicado en Immunology (2017)

Ligand-induced Ordering of the C-terminal Tail Primes STING for Phosphorylation by TBK1

por Tsuchiya, Yuko, Jounai, Nao, Takeshita, Fumihiko, Ishii, Ken J., Mizuguchi, Kenji
Publicado en EBioMedicine (2016)

Retinoblastoma-binding Protein 4-regulated Classical Nuclear Transport Is Involved in Cellular Senescence

por Tsujii, Akira, Miyamoto, Yoichi, Moriyama, Tetsuji, Tsuchiya, Yuko, Obuse, Chikashi, Mizuguchi, Kenji, Oka, Masahiro, Yoneda, Yoshihiro
Publicado en J Biol Chem (2015)

Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures

por Kinjo, Akira R., Bekker, Gert-Jan, Suzuki, Hirofumi, Tsuchiya, Yuko, Kawabata, Takeshi, Ikegawa, Yasuyo, Nakamura, Haruki
Publicado en Nucleic Acids Res (2017)

Visualization and quantitation of epidermal growth factor receptor homodimerization and activation with a proximity ligation assay

por Ota, Keiichi, Harada, Taishi, Otsubo, Kohei, Fujii, Akiko, Tsuchiya, Yuko, Tanaka, Kentaro, Okamoto, Isamu, Nakanishi, Yoichi
Publicado en Oncotarget (2017)

Actin Cytoskeletal Reorganization Function of JRAB/MICAL-L2 Is Fine-tuned by Intramolecular Interaction between First LIM Zinc Finger and C-terminal Coiled-coil Domains

por Miyake, Kazuhisa, Sakane, Ayuko, Tsuchiya, Yuko, Sagawa, Ikuko, Tomida, Yoko, Kasahara, Jiro, Imoto, Issei, Watanabe, Shio, Higo, Daisuke, Mizuguchi, Kenji, Sasaki, Takuya
Publicado en Sci Rep (2019)

Comprehensive analysis of PPARγ agonist activities of stereo-, regio-, and enantio-isomers of hydroxyoctadecadienoic acids

por Umeno, Aya, Sakashita, Mami, Sugino, Sakiko, Murotomi, Kazutoshi, Okuzawa, Tsugumi, Morita, Naoki, Tomii, Kentaro, Tsuchiya, Yuko, Yamasaki, Kazuhiko, Horie, Masanori, Takahara, Kentaro, Yoshida, Yasukazu
Publicado en Biosci Rep (2020)

Conformational plasticity of JRAB/MICAL-L2 provides “law and order” in collective cell migration

por Sakane, Ayuko, Yoshizawa, Shin, Nishimura, Masaomi, Tsuchiya, Yuko, Matsushita, Natsuki, Miyake, Kazuhisa, Horikawa, Kazuki, Imoto, Issei, Mizuguchi, Chiharu, Saito, Hiroyuki, Ueno, Takato, Matsushita, Sachi, Haga, Hisashi, Deguchi, Shinji, Mizuguchi, Kenji, Yokota, Hideo, Sasaki, Takuya
Publicado en Mol Biol Cell (2016)

New tools and functions in data‐out activities at Protein Data Bank Japan (PDBj)

por Kinjo, Akira R., Bekker, Gert‐Jan, Wako, Hiroshi, Endo, Shigeru, Tsuchiya, Yuko, Sato, Hiromu, Nishi, Hafumi, Kinoshita, Kengo, Suzuki, Hirofumi, Kawabata, Takeshi, Yokochi, Masashi, Iwata, Takeshi, Kobayashi, Naohiro, Fujiwara, Toshimichi, Kurisu, Genji, Nakamura, Haruki
Publicado en Protein Sci (2017)

Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target

por Chiba, Shuntaro, Ikeda, Kazuyoshi, Ishida, Takashi, Gromiha, M. Michael, Taguchi, Y-h., Iwadate, Mitsuo, Umeyama, Hideaki, Hsin, Kun-Yi, Kitano, Hiroaki, Yamamoto, Kazuki, Sugaya, Nobuyoshi, Kato, Koya, Okuno, Tatsuya, Chikenji, George, Mochizuki, Masahiro, Yasuo, Nobuaki, Yoshino, Ryunosuke, Yanagisawa, Keisuke, Ban, Tomohiro, Teramoto, Reiji, Ramakrishnan, Chandrasekaran, Thangakani, A. Mary, Velmurugan, D., Prathipati, Philip, Ito, Junichi, Tsuchiya, Yuko, Mizuguchi, Kenji, Honma, Teruki, Hirokawa, Takatsugu, Akiyama, Yutaka, Sekijima, Masakazu
Publicado en Sci Rep (2015)

Blind Prediction of Interfacial Water Positions in CAPRI

por Lensink, Marc F., Moal, Iain H., Bates, Paul A., Kastritis, Panagiotis L., Melquiond, Adrien S.J., Karaca, Ezgi, Schmitz, Christophe, van Dijk, Marc, Bonvin, Alexandre M.J.J., Eisenstein, Miriam, Jiménez-García, Brian, Grosdidier, Solène, Solernou, Albert, Pérez-Cano, Laura, Pallara, Chiara, Fernández-Recio, Juan, Xu, Jianqing, Muthu, Pravin, Kilambi, Krishna Praneeth, Gray, Jeffrey J., Grudinin, Sergei, Derevyanko, Georgy, Mitchell, Julie C., Wieting, John, Kanamori, Eiji, Tsuchiya, Yuko, Murakami, Yoichi, Sarmiento, Joy, Standley, Daron M., Shirota, Matsuyuki, Kinoshita, Kengo, Nakamura, Haruki, Chavent, Matthieu, Ritchie, David W., Park, Hahnbeom, Ko, Junsu, Lee, Hasup, Seok, Chaok, Shen, Yang, Kozakov, Dima, Vajda, Sandor, Kundrotas, Petras J., Vakser, Ilya A., Pierce, Brian G., Hwang, Howook, Vreven, Thom, Weng, Zhiping, Buch, Idit, Farkash, Efrat, Wolfson, Haim J., Zacharias, Martin, Qin, Sanbo, Zhou, Huan-Xiang, Huang, Shen-You, Zou, Xiaoqin, Wojdyla, Justyna A., Kleanthous, Colin, Wodak, Shoshana J.
Publicado en Proteins (2013)

Community-wide Evaluation of Methods for Predicting the Effect of Mutations on Protein-Protein Interactions

por Moretti, Rocco, Fleishman, Sarel J., Agius, Rudi, Torchala, Mieczyslaw, Bates, Paul A., Kastritis, Panagiotis L., Rodrigues, João P. G. L. M., Trellet, Mikaël, Bonvin, Alexandre M. J. J., Cui, Meng, Rooman, Marianne, Gillis, Dimitri, Dehouck, Yves, Moal, Iain, Romero-Durana, Miguel, Perez-Cano, Laura, Pallara, Chiara, Jimenez, Brian, Fernandez-Recio, Juan, Flores, Samuel, Pacella, Michael, Kilambi, Krishna Praneeth, Gray, Jeffrey J., Popov, Petr, Grudinin, Sergei, Esquivel-Rodríguez, Juan, Kihara, Daisuke, Zhao, Nan, Korkin, Dmitry, Zhu, Xiaolei, Demerdash, Omar N. A., Mitchell, Julie C., Kanamori, Eiji, Tsuchiya, Yuko, Nakamura, Haruki, Lee, Hasup, Park, Hahnbeom, Seok, Chaok, Sarmiento, Jamica, Liang, Shide, Teraguchi, Shusuke, Standley, Daron M., Shimoyama, Hiromitsu, Terashi, Genki, Takeda-Shitaka, Mayuko, Iwadate, Mitsuo, Umeyama, Hideaki, Beglov, Dmitri, Hall, David R., Kozakov, Dima, Vajda, Sandor, Pierce, Brian G., Hwang, Howook, Vreven, Thom, Weng, Zhiping, Huang, Yangyu, Li, Haotian, Yang, Xiufeng, Ji, Xiaofeng, Liu, Shiyong, Xiao, Yi, Zacharias, Martin, Qin, Sanbo, Zhou, Huan-Xiang, Huang, Sheng-You, Zou, Xiaoqin, Velankar, Sameer, Janin, Joël, Wodak, Shoshana J., Baker, David
Publicado 2013

Community-wide assessment of protein-interface modeling suggests improvements to design methodology

por Fleishman, Sarel J, Whitehead, Timothy A, Strauch, Eva-Maria, Corn, Jacob E, Qin, Sanbo, Zhou, Huan-Xiang, Mitchell, Julie C., Demerdash, Omar N.A, Takeda-Shitaka, Mayuko, Terashi, Genki, Moal, Iain H., Li, Xiaofan, Bates, Paul A., Zacharias, Martin, Park, Hahnbeom, Ko, Jun-su, Lee, Hasup, Seok, Chaok, Bourquard, Thomas, Bernauer, Julie, Poupon, Anne, Azé, Jérôme, Soner, Seren, Ovali, Şefik Kerem, Ozbek, Pemra, Ben Tal, Nir, Haliloglu, Türkan, Hwang, Howook, Vreven, Thom, Pierce, Brian G., Weng, Zhiping, Pérez-Cano, Laura, Pons, Carles, Fernández-Recio, Juan, Jiang, Fan, Yang, Feng, Gong, Xinqi, Cao, Libin, Xu, Xianjin, Liu, Bin, Wang, Panwen, Li, Chunhua, Wang, Cunxin, Robert, Charles H., Guharoy, Mainak, Liu, Shiyong, Huang, Yangyu, Li, Lin, Guo, Dachuan, Chen, Ying, Xiao, Yi, London, Nir, Itzhaki, Zohar, Schueler-Furman, Ora, Inbar, Yuval, Patapov, Vladimir, Cohen, Mati, Schreiber, Gideon, Tsuchiya, Yuko, Kanamori, Eiji, Standley, Daron M., Nakamura, Haruki, Kinoshita, Kengo, Driggers, Camden M., Hall, Robert G., Morgan, Jessica L., Hsu, Victor L., Zhan, Jian, Yang, Yuedong, Zhou, Yaoqi, Kastritis, Panagiotis L., Bonvin, Alexandre M.J.J., Zhang, Weiyi, Camacho, Carlos J., Kilambi, Krishna P., Sircar, Aroop, Gray, Jeffrey J., Ohue, Masahito, Uchikoga, Nobuyuki, Matsuzaki, Yuri, Ishida, Takashi, Akiyama, Yutaka, Khashan, Raed, Bush, Stephen, Fouches, Denis, Tropsha, Alexander, Esquivel-Rodríguez, Juan, Kihara, Daisuke, Stranges, P Benjamin, Jacak, Ron, Kuhlman, Brian, Huang, Sheng-You, Zou, Xiaoqin, Wodak, Shoshana J, Janin, Joel, Baker, David
Publicado 2011