LB3D: A Protein Three-Dimensional Substructure Search Program Based on the Lower Bound of a Root Mean Square Deviation Value. - Genki Terashi; Tetsuo Shibuya; Mayuko Takeda-Shitaka (J. Comput. Biol., 2012)

Protein Shape Retrieval. - Na Song; Daniela Craciun; Charles Christoffer; Xusi Han; Daisuke Kihara; Guillaume Levieux; Matthieu Montès; Hong Qin 001; Pranjal Sahu; Genki Terashi; Haiguang Liu (3DOR@Eurographics, 2017)

Modeling disordered protein interactions from biophysical principles. - Lenna X. Peterson; Amitava Roy; Charles Christoffer; Genki Terashi; Daisuke Kihara (PLoS Comput. Biol., 2017)

Modeling the assembly order of multimeric heteroprotein complexes. - Lenna X. Peterson; Yoichiro Togawa; Juan Esquivel-Rodríguez; Genki Terashi; Charles Christoffer; Amitava Roy; Woong-Hee Shin; Daisuke Kihara (PLoS Comput. Biol., 2018)

Classification in Cryo-Electron Tomograms. - Ilja Gubins; Gijs van der Schot; Remco C. Veltkamp; Friedrich Förster; Xuefeng Du; Xiangrui Zeng; Zhenxi Zhu; Lufan Chang; Min Xu 009; Emmanuel Moebel; Antonio Martínez-Sánchez; Charles Kervrann; et al. (3DOR@Eurographics, 2019)

Protein Shape Retrieval Contest. - Florent Langenfeld; Apostolos Axenopoulos; Halim Benhabiles; Petros Daras; Andrea Giachetti 001; Xusi Han; Karim Hammoudi; Daisuke Kihara; Tuan Manh Lai; Haiguang Liu; Mahmoud Melkemi; Stelios K. Mylonas; et al. (3DOR@Eurographics, 2019)

Study of the Variability of the Native Protein Structure. - Xusi Han; Woong-Hee Shin; Charles Christoffer; Genki Terashi; Lyman Monroe; Daisuke Kihara (Encyclopedia of Bioinformatics and Computational Biology (3), 2019)

Protein docking model evaluation by 3D deep convolutional neural networks. - Xiao Wang 013; Genki Terashi; Charles Christoffer; Mengmeng Zhu; Daisuke Kihara (Bioinform., 2020)

SHREC 2020: Multi-domain protein shape retrieval challenge. - Florent Langenfeld; Yuxu Peng; Yu-Kun Lai; Paul L. Rosin; Tunde Aderinwale; Genki Terashi; Charles Christoffer; Daisuke Kihara; Halim Benhabiles; Karim Hammoudi; Adnane Cabani; Féryal Windal; et al. (Comput. Graph., 2020)

MAINMASTseg: Automated Map Segmentation Method for Cryo-EM Density Maps with Symmetry. - Genki Terashi; Yuki Kagaya; Daisuke Kihara (J. Chem. Inf. Model., 2020)

Path-LZerD: Predicting Assembly Order of Multimeric Protein Complexes. - Genki Terashi; Charles Christoffer; Daisuke Kihara (Protein-Protein Interaction Networks, 2020)

SHREC 2021: Surface-based Protein Domains Retrieval. - Florent Langenfeld; Tunde Aderinwale; Charles Christoffer; Woong-Hee Shin; Genki Terashi; Xiao Wang 004; Daisuke Kihara; Halim Benhabiles; Karim Hammoudi; Adnane Cabani; Féryal Windal; Mahmoud Melkemi; et al. (3DOR, 2021)

Protein contact map refinement for improving structure prediction using generative adversarial networks. - Sai Raghavendra Maddhuri Venkata Subramaniya; Genki Terashi; Aashish Jain; Yuki Kagaya; Daisuke Kihara (Bioinform., 2021)

Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps. - Takaharu Mori; Genki Terashi; Daisuke Matsuoka; Daisuke Kihara; Yuji Sugita (J. Chem. Inf. Model., 2021)

Enhancing cryo-EM maps with 3D deep generative networks for assisting protein structure modeling. - Sai Raghavendra Maddhuri Venkata Subramaniya; Genki Terashi; Daisuke Kihara (Bioinform., 2023)