Decoupling Architecture for All-to-all Computation. - Atsushi Hori; Kazumi Yoshinaga; Atsushi Tokuhisa; Yasumasa Joti; Kensuke Okada; Takashi Sugimoto; Mitsuhiro Yamaga; Takaki Hatsui; Makina Yabashi; Yuji Sugita; Yutaka Ishikawa; Nobuhiro Go (EuroMPI/ASIA, 2014)

High-Precision Atomic Charge Prediction for Protein Systems Using Fragment Molecular Orbital Calculation and Machine Learning. - Koichiro Kato; Tomohide Masuda; Chiduru Watanabe; Naoki Miyagawa; Hideo Mizouchi; Shumpei Nagase; Kikuko Kamisaka; Kanji Oshima; Satoshi Ono; Hiroshi Ueda; Atsushi Tokuhisa; Ryo Kanada; et al. (J. Chem. Inf. Model., 2020)

Coarse-Grained Diffraction Template Matching Model to Retrieve Multiconformational Models for Biomolecule Structures from Noisy Diffraction Patterns. - Atsushi Tokuhisa; Ryo Kanada; Shuntaro Chiba; Kei Terayama; Yuta Isaka; Biao Ma; Narutoshi Kamiya; Yasushi Okuno (J. Chem. Inf. Model., 2020)

Protein-ligand binding affinity prediction of cyclin-dependent kinase-2 inhibitors by dynamically averaged fragment molecular orbital-based interaction energy. - Kenichiro Takaba; Chiduru Watanabe; Atsushi Tokuhisa; Yoshinobu Akinaga; Biao Ma; Ryo Kanada; Mitsugu Araki; Yasushi Okuno; Yusuke Kawashima; Hirotomo Moriwaki; Norihito Kawashita; Teruki Honma; et al. (J. Comput. Chem., 2022)

Single-Image Super-Resolution Improvement of X-ray Single-Particle Diffraction Images Using a Convolutional Neural Network. - Atsushi Tokuhisa; Yoshinobu Akinaga; Kei Terayama; Yuji Okamoto; Yasushi Okuno (J. Chem. Inf. Model., 2022)

Accelerating AlphaFold2 Inference of Protein Three-Dimensional Structure on the Supercomputer Fugaku. - Yosuke Oyama; Akihiro Tabuchi; Atsushi Tokuhisa (FlexScience@HPDC, 2023)

An Auto-Encoder to Reconstruct Structure with Cryo-EM Images via Theoretically Guaranteed Isometric Latent Space, and Its Application for Automatically Computing the Conformational Pathway. - Kimihiro Yamazaki; Yuichiro Wada; Atsushi Tokuhisa; Mutsuyo Wada; Takashi Katoh; Yuhei Umeda; Yasushi Okuno; Akira Nakagawa (MICCAI (1), 2023)

Investigating self-supervised image denoising with denaturation. - Hiroki Waida; Kimihiro Yamazaki; Atsushi Tokuhisa; Mutsuyo Wada; Yuichiro Wada (Neural Networks, 2025)