Ligand-binding site prediction of proteins based on known fragment-fragment interactions. - Kota Kasahara; Kengo Kinoshita; Toshihisa Takagi (Bioinform., 2010)

Comprehensive Classification and Diversity Assessment of Atomic Contacts in Protein-Small Ligand Interactions. - Kota Kasahara; Matsuyuki Shirota; Kengo Kinoshita (J. Chem. Inf. Model., 2013)

GIANT: pattern analysis of molecular interactions in 3D structures of protein-small ligand complexes. - Kota Kasahara; Kengo Kinoshita (BMC Bioinform., 2014)

Development of Superconducting Tunnel Junction detectors as a far-infrared photon-by-photon spectrometer for neutrino decay search. - Yuji Takeuchi; Shin-Hong Kim; Kenichi Takemasa; Kenji Kiuchi; Kazuki Nagata; Kota Kasahara; Takuya Okudaira; Tatsuya Ichimura; Masahiro Kanamaru; Kouya Moriuchi; Ren Senzaki; Shunsuke Yagi; et al. (I2MTC, 2015)

Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking. - Junichi Higo; Bhaskar Dasgupta; Tadaaki Mashimo; Kota Kasahara; Yoshifumi Fukunishi; Haruki Nakamura (J. Comput. Chem., 2015)

Architecture of an FPGA accelerator for molecular dynamics simulation using OpenCL. - Hasitha Muthumala Waidyasooriya; Masanori Hariyama; Kota Kasahara (ICIS, 2016)

mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories. - Kota Kasahara; Neetha Mohan; Ikuo Fukuda; Haruki Nakamura (Bioinform., 2016)

An FPGA Accelerator for Molecular Dynamics Simulation Using OpenCL. - Hasitha Muthumala Waidyasooriya; Masanori Hariyama; Kota Kasahara (Int. J. Networked Distributed Comput., 2017)

Molecular dynamics coupled with a virtual system for effective conformational sampling. - Tomonori Hayami; Kota Kasahara; Haruki Nakamura; Junichi Higo (J. Comput. Chem., 2018)

Multidimensional virtual-system coupled canonical molecular dynamics to compute free-energy landscapes of peptide multimer assembly. - Tomonori Hayami; Junichi Higo; Haruki Nakamura; Kota Kasahara (J. Comput. Chem., 2019)

Molecular Interaction Mechanism of a 14-3-3 Protein with a Phosphorylated Peptide Elucidated by Enhanced Conformational Sampling. - Junichi Higo; Takeshi Kawabata; Ayumi Kusaka; Kota Kasahara; Narutoshi Kamiya; Ikuo Fukuda; Kentaro Mori; Yutaka Hata; Yoshifumi Fukunishi; Haruki Nakamura (J. Chem. Inf. Model., 2020)

Extended ensemble simulations of a SARS-CoV-2 nsp1-5'-UTR complex. - Shun Sakuraba; Qilin Xie; Kota Kasahara; Junichi Iwakiri; Hidetoshi Kono (PLoS Comput. Biol., 2022)