Exhaustive search of the configurational space of heat‐shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking von Bekker, Gert‐Jan, Araki, Mitsugu, Oshima, Kanji, Okuno, Yasushi, Kamiya, Narutoshi

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Thermal stability of single‐domain antibodies estimated by molecular dynamics simulations von Bekker, Gert‐Jan, Ma, Benson, Kamiya, Narutoshi

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Structural basis of mutants of PET‐degrading enzyme from Saccharomonospora viridis AHK190 with high activity and thermal stability von Emori, Miho, Numoto, Nobutaka, Senga, Akane, Bekker, Gert‐Jan, Kamiya, Narutoshi, Kobayashi, Yuma, Ito, Nobutoshi, Kawai, Fusako, Oda, Masayuki

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N‑Terminal-Driven Binding Mechanism of an Antigen Peptide to Human Leukocyte Antigen-A2402 Elucidated by Multicanonical Molecular Dynamic-Based Dynamic Docking and Path Sampling Si... von Bekker, Gert-Jan, Kamiya, Narutoshi

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Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data von Bekker, Gert‐Jan, Yokochi, Masashi, Suzuki, Hirofumi, Ikegawa, Yasuyo, Iwata, Takeshi, Kudou, Takahiro, Yura, Kei, Fujiwara, Toshimichi, Kawabata, Takeshi, Kurisu, Genji

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

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The Biological Structure Model Archive (BSM-Arc): an archive for in silico models and simulations von Bekker, Gert-Jan, Kawabata, Takeshi, Kurisu, Genji

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New tools and functions in data‐out activities at Protein Data Bank Japan (PDBj) von Kinjo, Akira R., Bekker, Gert‐Jan, Wako, Hiroshi, Endo, Shigeru, Tsuchiya, Yuko, Sato, Hiromu, Nishi, Hafumi, Kinoshita, Kengo, Suzuki, Hirofumi, Kawabata, Takeshi, Yokochi, Masashi, Iwata, Takeshi, Kobayashi, Naohiro, Fujiwara, Toshimichi, Kurisu, Genji, Nakamura, Haruki

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Cryptic-site binding mechanism of medium-sized Bcl-xL inhibiting compounds elucidated by McMD-based dynamic docking simulations von Bekker, Gert-Jan, Fukuda, Ikuo, Higo, Junichi, Fukunishi, Yoshifumi, Kamiya, Narutoshi

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Cutinases from thermophilic bacteria (actinomycetes): From identification to functional and structural characterization von Oda, Masayuki, Numoto, Nobutaka, Bekker, Gert-Jan, Kamiya, Narutoshi, Kawai, Fusako

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Accurate Prediction of Complex Structure and Affinity for a Flexible Protein Receptor and Its Inhibitor von Bekker, Gert-Jan, Kamiya, Narutoshi, Araki, Mitsugu, Fukuda, Ikuo, Okuno, Yasushi, Nakamura, Haruki

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Thermal Stability Estimation of Single Domain Antibodies Using Molecular Dynamics Simulations von Bekker, Gert-Jan, Kamiya, Narutoshi

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Binding Mechanism of Riboswitch to Natural Ligand Elucidated by McMD-Based Dynamic Docking Simulations von Bekker, Gert-Jan, Fukunishi, Yoshifumi, Higo, Junichi, Kamiya, Narutoshi

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Mutual induced-fit mechanism drives binding between intrinsically disordered Bim and cryptic binding site of Bcl-xL von Bekker, Gert-Jan, Araki, Mitsugu, Oshima, Kanji, Okuno, Yasushi, Kamiya, Narutoshi

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Binding free-energy landscapes of small molecule binder and non-binder to FMN riboswitch: All-atom molecular dynamics von Higo, Junichi, Bekker, Gert-Jan, Kamiya, Narutoshi, Fukuda, Ikuo, Fukunishi, Yoshifumi

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Structural Dynamics of the PET-Degrading Cutinase-like Enzyme from Saccharomonospora viridis AHK190 in Substrate-Bound States Elucidates the Ca2+-Driven Catalytic Cycle von Numoto, Nobutaka, Kamiya, Narutoshi, Bekker, Gert-Jan, Yamagami, Yuri, Inaba, Satomi, Ishii, Kentaro, Uchiyama, Susumu, Kawai, Fusako, Ito, Nobutoshi, Oda, Masayuki

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Manipulation of L-ascorbic acid biosynthesis pathways in Solanum lycopersicum: elevated GDP-mannose pyrophosphorylase activity enhances L-ascorbate levels in red fruit von Cronje, Christelle, George, Gavin M., Fernie, Alisdair R., Bekker, Jan, Kossmann, Jens, Bauer, Rolene

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Molmil: a molecular viewer for the PDB and beyond von Bekker, Gert-Jan, Nakamura, Haruki, Kinjo, Akira R.

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History of Protein Data Bank Japan: standing at the beginning of the age of structural genomics von Kurisu, Genji, Bekker, Gert-Jan, Nakagawa, Atsushi

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Exopolysaccharide production by lactose-hydrolyzing bacteria isolated from traditionally fermented milk von Bauer, Rolene, Bekker, Jan P., Wyk, Nathan van, du Toit, Christian, Dicks, Leon M.T., Kossmann, Jens

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