Method for Systematic Analogue Search Using the Mega SAR Matrix Database. - Atsushi Yoshimori; Yuichi Horita; Toru Tanoue; Jürgen Bajorath (J. Chem. Inf. Model., 2019)

Adapting the DeepSARM approach for dual-target ligand design. - Atsushi Yoshimori; Huabin Hu; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2021)

Generalized-ensemble method study: A helix-mimetic compound inhibits protein-protein interaction by long-range and short-range intermolecular interactions. - Junichi Higo; Hajime Takashima; Yoshifumi Fukunishi; Atsushi Yoshimori (J. Comput. Chem., 2021)

Candidate compounds from the design of covalent Bruton's tyrosine kinase (BTK) inhibitors via focused deep generative modeling. - Atsushi Yoshimori; Filip Miljkovic; Jürgen Bajorath (Zenodo, 2022)

DeepCubist: Molecular Generator for Designing Peptidomimetics based on Complex three-dimensional scaffolds. - Kohei Umedera; Atsushi Yoshimori; Hengwei Chen; Hiroyuki Kouji; Hiroyuki Nakamura; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2023)

Context-dependent similarity analysis of analogue series for structure-activity relationship transfer based on a concept from natural language processing. - Atsushi Yoshimori; Jürgen Bajorath (J. Cheminformatics, 2025)

Context-dependent similarity searching for small molecular fragments. - Atsushi Yoshimori; Jürgen Bajorath (J. Cheminformatics, 2025)