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The Journal of Physical Chemistry. B|July 18, 2008
Special pair dance and partner selection: elementary steps in proton transport in liquid waterOmer Markovitch, Hanning Chen, Sergei Izvekov, et al.The Journal of Physical Chemistry. A|May 20, 2009
Distance-dependent proton transfer along water wires connecting acid-base pairsM Jocelyn Cox, Rutger L A Timmer, Huib J Bakker, et al.Biophysics and Physicobiology|January 28, 2020
Building a macro-mixing dual-basin Gō model using the Multistate Bennett Acceptance RatioAi Shinobu, Chigusa Kobayashi, Yasuhiro Matsunaga, et al.The Journal of Chemical Physics|November 24, 2018
Refining evERdock: Improved selection of good protein-protein complex models achieved by MD optimization and use of multiple conformationsAi Shinobu, Kazuhiro Takemura, Nobuyuki Matubayasi, et al.Journal of Chemical Information and Modeling|May 6, 2021
Coarse-Grained Modeling of Multiple Pathways in Conformational Transitions of Multi-Domain ProteinsAi Shinobu, Chigusa Kobayashi, Yasuhiro Matsunaga, et al.The Journal of Chemical Physics|December 12, 2019
evERdock BAI: Machine-learning-guided selection of protein-protein complex structureKei Terayama, Ai Shinobu, Koji Tsuda, et al.The Journal of Physical Chemistry. B|March 17, 2021
Unraveling the Coupling between Conformational Changes and Ligand Binding in Ribose Binding Protein Using Multiscale Molecular Dynamics and Free-Energy CalculationsWeitong Ren, Hisham M Dokainish, Ai Shinobu, et al.Chemical Reviews|June 18, 2016
Protons and Hydroxide Ions in Aqueous SystemsNoam Agmon, Huib J Bakker, R Kramer Campen, et al.Proceedings of the National Academy of Sciences of the United States of America|April 5, 2024
Molecular dynamics in multidimensional space explains how mutations affect the association path of neomycin to a riboswitchPiotr Chyży, Marta Kulik, Ai Shinobu, et al.Scientific Reports|July 5, 2017
Origin of proton affinity to membrane/water interfacesEwald Weichselbaum, Maria Österbauer, Denis G Knyazev, et al.Pageof 7