Protein ligand binding site prediction using graph transformer neural network

Ryuichiro Ishitani ,Mizuki Takemoto and Kentaro Tomii

PLOS ONE(2024)

doi:10.1371/journal.pone.0308425

Neuronal and non-neuronal functions of the synaptic cell adhesion molecule neurexin in Nematostella vectensis

Christine Guzman, Kurato Mohri, Ryotaro Nakamura, Minato Miyake, Yuko Tsuchiya, Kentaro Tomii and Hiroshi Watanabe

Nat. Commun.(2024) 15(1) 6495.

doi:10.1038/s41467-024-50818-8

PoSSuM v.3: A Major Expansion of the PoSSuM Database for Finding Similar Binding Sites of Proteins

Yuko Tsuchiya, Tomoki Yonezawa, Yu Yamamori, Hiroko Inoura, Masanori Osawa, Kazuyoshi Ikeda, and Kentaro Tomii

J. Chem. Inf. Model.(2023).

doi:10.1021/acs.jcim.3c01405

Predicting global distributions of eukaryotic plankton communities from satellite data

Hiroto Kaneko, Hisashi Endo, Nicolas Henry, Cédric Berney, Frédéric Mahé, Julie Poulain, Karine Labadie, Odette Beluche, Roy El Hourany, Tara Oceans Coordinators, Samuel Chaffron, Patrick Wincker, Ryosuke Nakamura, Lee Karp-Boss, Emmanuel Boss, Chris Bowler, Colomban de Vargas, Kentaro Tomii, Hiroyuki Ogata  

ISME COMMUN. 3, 101(2023).

doi:10.1038/s43705-023-00308-7

A multipoint guidance mechanism for β-barrel folding on the SAM complex

Hironori Takeda, Jon V. Busto, Caroline Lindau, Akihisa Tsutsumi, Kentaro Tomii, Kenichiro Imai, Yu Yamamori, Takatsugu Hirokawa, Chie Motono, Iniyan Ganesan, Lena-Sophie Wenz, Thomas Becker, Masahide Kikkawa, Nikolaus Pfanner, Nils Wiedemann, Toshiya Endo 

Nat Struct Mol Biol(2023).

doi:10.1038/s41594-022-00897-2

Protein-protein interaction prediction methods: from docking-based to AI-based approaches

Yuko Tsuchiya, Yu Yamamori, Kentaro Tomii

Biophysical Reviews(2022).

doi:10.1007/s12551-022-01032-7

Distinct immune cell dynamics correlate with the immunogenicity and reactogenicity of SARS-CoV-2 mRNA vaccine

Tomohiro Takano, Miwa Morikawa, Yu Adachi, Kiyomi Kabasawa, Nicolas Sax, Saya Moriyama, Lin Sun, Masanori Isogawa, Ayae Nishiyama, Taishi Onodera, Kazutaka Terahara, Keisuke Tonouchi, Masashi Nishimura, Kentaro Tomii, Kazuo Yamashita, Takayuki Matsumura, Masaharu Shinkai, Yoshimasa Takahashi

Cell Rep Med.17;3(5):100631 (2022).

doi:10.1016/j.xcrm.2022.100631.

Structure-based analyses of gut microbiome-related proteins by neural networks and molecular dynamics simulations.

Taneishi K, Tsuchiya Y.

Curr Opin Struct Biol. 2022 Apr;73:102336

doi:10.1016/j.sbi.2022.102336

Application of Homology Modeling by Enhanced Profile-Profile Alignment and Flexible-Fitting Simulation to Cryo-EM Based Structure Determination

Yu Yamamori, Kentaro Tomii

Int. J. Mol. Sci. 23, 1977, (2022)

doi:10.3390/ijms23041977

Crystal structure of Tam41 cytidine diphosphate diacylglycerol synthase from a Firmicutes bacterium

Keisuke Kimura, Fumihiro Kawai, Hisako Kubota-Kawai, Yasunori Watanabe, Kentaro Tomii, Rieko Kojima, Kunio Hirata, Yu Yamamori, Toshiya Endo, Yasushi Tamura

J. Biochem. 29 December (2021)

doi:10.1093/jb/mvab154