Molmil: a molecular viewer for the PDB and beyond. - Gert-Jan Bekker; Haruki Nakamura; Akira R. Kinjo (J. Cheminformatics, 2016)

Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures. - Akira R. Kinjo; Gert-Jan Bekker; Hirofumi Suzuki; Yuko Tsuchiya; Takeshi Kawabata; Yasuyo Ikegawa; Haruki Nakamura (Nucleic Acids Res., 2017)

Exhaustive search of the configurational space of heat-shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking. - Gert-Jan Bekker; Mitsugu Araki; Kanji Oshima; Yasushi Okuno; Narutoshi Kamiya (J. Comput. Chem., 2020)

Accurate Binding Configuration Prediction of a G-Protein-Coupled Receptor to Its Antagonist Using Multicanonical Molecular Dynamics-Based Dynamic Docking. - Gert-Jan Bekker; Mitsugu Araki; Kanji Oshima; Yasushi Okuno; Narutoshi Kamiya (J. Chem. Inf. Model., 2021)

Binding Mechanism between Platelet Glycoprotein and Cyclic Peptide Elucidated by McMD-Based Dynamic Docking. - Gert-Jan Bekker; Kanji Oshima; Mitsugu Araki; Yasushi Okuno; Narutoshi Kamiya (J. Chem. Inf. Model., 2024)