2026年
論文
- Tatsuki Hori, Yoshitaka Moriwaki, Ryuichiro Ishitani, Distance-Restraint-Guided Diffusion Models for Sampling Protein Conformational Changes and Ligand Dissociation Pathways, J. Chem. Theory Comput., DOI:10.1021/acs.jctc.6c00199, (2026).
- Nayuta Nagano, Koichi Kiuchi, Atsushi Minato, Shusuke Sato, Yoshitaka Moriwaki, Rolf Müller, Tadashi Eguchi, Fumitaka Kudo, 4″-Methyl-S-Adenosyl-l-Methionines Are Substrates for 4-Methylazetidinecarboxylic Acid Synthases, ACS Chemical Biology, DOI:10.1021/acschembio.5c00642, (2026).
- Ryo Akiba, Yoshitaka Moriwaki, Ryuichiro Ishitani, Naruki Yoshikawa, Multi-objective optimization for designing structurally similar proteins with diverse sequences, Science and Technology of Advanced Materials: Methods, DOI:10.1080/27660400.2025.2611575, (2026).
- Yiming Zhang, Ryuichiro Ishitani, Mizuki Takemoto, Atsuhiro Tomita, Generalizable compound protein interaction prediction with a model incorporating protein structure aware and compound property aware language model representations, Communications Chemistry, 9, 37 DOI: 10.1038/s42004-025-01844-0, (2026)
2025年
論文
- Ryuichiro Ishitani, Yoshitaka Moriwaki, Improving Stereochemical Limitations in Protein-Ligand Complex Structure Prediction, ACS Omega, 10(46), 56075–56084, DOI:10.1021/acsomega.5c07675, (2025).
- Yoshitaka Moriwaki, Taro Shiraishi, Yohei Katsuyama, Kenichi Matsuda, Toyoyuki Ose, Atsushi Minami, Hideaki Oikawa, Tomohisa Kuzuyama, Ryuichiro Ishitani, Tohru Terada Predicting protein complexes in biosynthetic gene clusters, bioRxiv, DOI:10.1101/2025.10.26.684697, (2025).
- Andrew I. Cooper, Patrick Courtney, Kourosh Darvish, Moritz Eckhoff, Hatem Fakhruldeen, Andrea Gabrielli, Animesh Garg, Sami Haddadin, Kanako Harada, Jason Hein, Maria Hübner, Dennis Knobbe, Gabriella Pizzuto, Florian Shkurti, Ruja Shrestha, Kerstin Thurow, Rafael Vescovi, Birgit Vogel-Heuser, Ádám Wolf, Naruki Yoshikawa, Yan Zeng, Zhengxue Zhou, Henning Zwirnmann, Accelerating discovery in natural science laboratories with AI and robotics: Perspectives and challenges, Science Robotics, 10, eadv7932, DOI: 10.1126/scirobotics.adv7932, (2025).
- Aiko Watanabe, Shizuka Ogiwara, Mirei Saito, Masaki Mishima, Masahiro Yamashina, Ryuichiro Ishitani, Yutaka Ito, Keiji Tanaka, Fumika Koyano, Koji Yamano, Hidetaka Kosako, Yoshitaka Moriwaki, Noriyuki Matsuda, The reaction mechanism for glycolysis side product degradation by Parkinson’s disease-linked DJ-1, J. Cell. Biol., 224(8), e202411078, DOI:10.1083/jcb.202411078, (2025).
- Naruki Yoshikawa, Yuki Asano, Don N. Futaba, Kanako Harada, Taro Hitosugi, Genki N. Kanda, Shoichi Matsuda, Yuuya Nagata, Keisuke Nagato, Masanobu Naito, Tohru Natsume, Kazunori Nishio, Kanta Ono, Haruka Ozaki, Woosuck Shin, Junichiro Shiomi, Kunihiko Shizume, Koichi Takahashi, Seiji Takeda, Ichiro Takeuchi, Ryo Tamura, Koji Tsuda, Yoshitaka Ushiku, Self-driving laboratories in Japan, Digital Discovery, 4, 1384-1403, DOI:10.1039/d4dd00387j, (2025).
- Seiji Kawai, Masayuki Karasawa, Yoshitaka Moriwaki, Tohru Terada, Yohei Katsuyama, Yasuo Ohnishi, Structural Basis for the Catalytic Mechanism of ATP-Dependent Diazotase CmaA6, Angew. Chem. Int. Ed. e202505851, DOI:10.1002/anie.202505851, (2025).
- Fumiya K Sano, Kota Shimizume, Kazuhiro Kobayashi, Toshikuni Awazu, Kouki Kawakami, Hiroaki Akasaka, Takaaki A Kobayashi, Tatsuki Tanaka, Hiroyuki H Okamoto, Hisato Hirano, Tsukasa Kusakizako, Wataru Shihoya, Yoshiaki Kise, Yuzuru Itoh, Ryuichiro Ishitani, Yasushi Okada, Yasushi Sako, Masataka Yanagawa, Asuka Inoue, Osamu Nureki, Insights into G-protein coupling preference from cryo-EM structures of Gq-bound PTH1R, Nat. Chem. Biol. 21, 1906–1914,DOI: 10.1038/s41589-025-01957-6 (2025).
学会発表
シンポジウム等
- 堀 立樹, 森脇 由隆, 石谷 隆一郎、拘束条件付き複合体構造予測による構造サンプリング、学術変革領域研究 (A) 予知生合成科学 2025年 若手合宿勉強会 2025年9月7日 (日) ‒ 9月8日 (月) タカオネ 〒193-0844 東京都八王子市高尾町2264
- 堀立樹、森脇由隆、石谷隆一郎、Structural Sampling with Distance Restrained Biomolecular Complex Structure Prediction Model、学術変革領域 A 蛋白質新機能生成第4回領域会議、 2025 年 12 月 8-9 日、淡路夢舞台国際会議場
2024年
論文
- Takahiro Mori, Yoshitaka Moriwaki, Kousuke Sakurada, Shuang Lyu, Stanislav Kadlcik, Jiri Janata, Aninda Mazumdar, Markéta Koběrská, Tohru Terada, Zdenek Kamenik, Ikuro Abe Molecular basis for the diversification of lincosamide biosynthesis by pyridoxal phosphate-dependent enzymes, Nature Chemistry, DOI: 10.1038/s41557-024-01687-7, (2024).
- Gyuri Kim, Sewon Lee, Eli Levy Karin, Hyunbin Kim, Yoshitaka Moriwaki, Sergey Ovchinnikov, Martin Steinegger, Milot Mirdita, Easy and accurate protein structure prediction using ColabFold, Nature Protocols, DOI: 10.1038/s41596-024-01060-5, (2024).
- Masato Homma, Takatoshi Wakabayashi, Yoshitaka Moriwaki, Takumi Shigeta, Kazuki Isobe, Atsushi Okazawa, Daisaku Ohta, Tohru Terada, Kentaro Shimizu, Masaharu Mizutani, Hirosato Takikawa, Yukihiro Sugimoto, Insights into stereoselective ring formation in canonical strigolactone: Identification of a dirigent domain-containing enzyme catalyzing orobanchol synthesis, Proc. Natl. Acad. Sci. USA, 121, e2313683121, DOI: 10.1073/pnas.2313683121, (2024).
- Ryuichiro Ishitani, Mizuki Takemoto, Kentaro Tomii, Protein ligand binding site prediction using graph transformer neural network, PLoS ONE, 19(8), e0308425, DOI:10.1371/journal.pone.0308425, (2024).