Thermal stability of single‐domain antibodies estimated by molecular dynamics simulations

por Bekker, Gert‐Jan, Ma, Benson, Kamiya, Narutoshi
Publicado 2018

The Biological Structure Model Archive (BSM-Arc): an archive for in silico models and simulations

por Bekker, Gert-Jan, Kawabata, Takeshi, Kurisu, Genji
Publicado 2020

History of Protein Data Bank Japan: standing at the beginning of the age of structural genomics

por Kurisu, Genji, Bekker, Gert-Jan, Nakagawa, Atsushi
Publicado 2022

Molmil: a molecular viewer for the PDB and beyond

por Bekker, Gert-Jan, Nakamura, Haruki, Kinjo, Akira R.
Publicado 2016

Mutual population-shift driven antibody-peptide binding elucidated by molecular dynamics simulations

por Bekker, Gert-Jan, Fukuda, Ikuo, Higo, Junichi, Kamiya, Narutoshi
Publicado 2020

Mutual induced-fit mechanism drives binding between intrinsically disordered Bim and cryptic binding site of Bcl-xL

por Bekker, Gert-Jan, Araki, Mitsugu, Oshima, Kanji, Okuno, Yasushi, Kamiya, Narutoshi
Publicado 2023

Cryptic-site binding mechanism of medium-sized Bcl-xL inhibiting compounds elucidated by McMD-based dynamic docking simulations

por Bekker, Gert-Jan, Fukuda, Ikuo, Higo, Junichi, Fukunishi, Yoshifumi, Kamiya, Narutoshi
Publicado 2021

Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics

por Araki, Mitsugu, Matsumoto, Shigeyuki, Bekker, Gert-Jan, Isaka, Yuta, Sagae, Yukari, Kamiya, Narutoshi, Okuno, Yasushi
Publicado 2021

Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures

por Kinjo, Akira R., Bekker, Gert-Jan, Suzuki, Hirofumi, Tsuchiya, Yuko, Kawabata, Takeshi, Ikegawa, Yasuyo, Nakamura, Haruki
Publicado 2017

Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data

por Bekker, Gert‐Jan, Yokochi, Masashi, Suzuki, Hirofumi, Ikegawa, Yasuyo, Iwata, Takeshi, Kudou, Takahiro, Yura, Kei, Fujiwara, Toshimichi, Kawabata, Takeshi, Kurisu, Genji
Publicado 2021

Fly casting with ligand sliding and orientational selection supporting complex formation of a GPCR and a middle sized flexible molecule

por Higo, Junichi, Kasahara, Kota, Bekker, Gert-Jan, Ma, Benson, Sakuraba, Shun, Iida, Shinji, Kamiya, Narutoshi, Fukuda, Ikuo, Kono, Hidetoshi, Fukunishi, Yoshifumi, Nakamura, Haruki
Publicado 2022

New tools and functions in data‐out activities at Protein Data Bank Japan (PDBj)

por 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
Publicado 2017