Toru Ekimoto

发表

Combination of coarse-grained molecular dynamics simulations and small-angle X-ray scattering experiments

M. Ikeguchi, Toru Ekimoto, Yuichi Kokabu, 2019, Biophysics and physicobiology.

Hybrid Methods for Modeling Protein Structures Using Molecular Dynamics Simulations and Small-Angle X-Ray Scattering Data.

M. Ikeguchi, Toru Ekimoto, 2018, Advances in experimental medicine and biology.

Multiscale molecular dynamics simulations of rotary motor proteins

M. Ikeguchi, Toru Ekimoto, 2017, Biophysical Reviews.

Finite-size effect on the charging free energy of protein in explicit solvent.

M. Ikeguchi, N. Matubayasi, Toru Ekimoto, 2015, Journal of chemical theory and computation.

Rotation Mechanism of Molecular Motor V1-ATPase Studied by Multiscale Molecular Dynamics Simulation

M. Ikeguchi, Toru Ekimoto, Yuichi Kokabu, 2017, Biophysical journal.

Fast and slow relaxations in the free energy landscape

T. Odagaki, Toru Ekimoto, 2007 .

Serine 298 Phosphorylation in Linker 2 of UHRF1 Regulates Ligand-Binding Property of its Tandem Tudor Domain.

M. Ikeguchi, Miwa Sato, Toru Ekimoto, 2020, Journal of molecular biology.

Structure of SARS-CoV-2 membrane protein essential for virus assembly

M. Ikeguchi, S. Iwata, Takeshi Noda, 2022, Nature Communications.

Supramolecular Mechanosensitive Potassium Channel Formed by Fluorinated Amphiphilic Cyclophane.

T. Yamane, M. Ikeguchi, H. Noji, 2022, Journal of the American Chemical Society.

Hybrid in vitro/in silico analysis of low‐affinity protein–protein interactions that regulate signal transduction by Sema6D

T. Yamane, M. Ikeguchi, S. Akashi, 2022, Protein science : a publication of the Protein Society.

Binding and unbinding pathways of peptide substrate on SARS-CoV-2 3CL protease

A. Kidera, K. Moritsugu, M. Ikeguchi, 2022, bioRxiv.

Rotational Mechanism Model of the Bacterial V1 Motor Based on Structural and Computational Analyses

C. Chipot, M. Ikeguchi, A. Singharoy, 2019, Front. Physiol..

Functional dynamics of SARS-CoV-2 3C-like protease as a member of clan PA

A. Kidera, K. Moritsugu, M. Ikeguchi, 2022, Biophysical Reviews.

Imidazolinium-based Multiblock Amphiphile as Transmembrane Anion Transporter.

M. Ikeguchi, H. Noji, Toru Ekimoto, 2020, Chemistry, an Asian journal.

An accurate and rapid method for calculating hydration free energies of a variety of solutes including proteins.

M. Ikeguchi, Toru Ekimoto, Tomohiko Hayashi, 2019, The Journal of chemical physics.

An accurate and efficient computation method of the hydration free energy of a large, complex molecule.

M. Ikeguchi, N. Matubayasi, Toru Ekimoto, 2015, The Journal of chemical physics.

Structure-based screening combined with computational and biochemical analyses identified the inhibitor targeting the binding of DNA Ligase 1 to UHRF1.

P. Defossez, K. Tsumoto, M. Ikeguchi, 2021, Bioorganic & medicinal chemistry.

Functional dynamics of SARS-CoV-2 3C-like protease as a member of clan PA

A. Kidera, K. Moritsugu, M. Ikeguchi, 2022, Biophysical Reviews.

Allosteric Regulation of 3CL Protease of SARS-CoV-2 and SARS-CoV Observed in the Crystal Structure Ensemble

A. Kidera, K. Moritsugu, M. Ikeguchi, 2021, bioRxiv.

TLR3 forms a laterally aligned multimeric complex along double-stranded RNA for efficient signal transduction

M. Ikeguchi, H. Shigematsu, Toshiyuki Shimizu, 2023, Nature Communications.

Structural and dynamical insights into the PH domain of p62 in human TFIIH

M. Ikeguchi, Toru Ekimoto, Y. Nishimura, 2020, Nucleic acids research.

Binding and Unbinding Pathways of Peptide Substrates on the SARS-CoV-2 3CL Protease

A. Kidera, K. Moritsugu, M. Ikeguchi, 2022, J. Chem. Inf. Model..

Moving toward generalizable NZ-1 labeling for 3D structure determination with optimized epitope-tag insertion

M. Ikeguchi, Toru Ekimoto, T. Nogi, 2021, Acta crystallographica. Section D, Structural biology.

Moving toward generalizable NZ-1 labeling for 3D structure determination with optimized epitope tag insertion

M. Ikeguchi, Toru Ekimoto, T. Nogi, 2020, bioRxiv.

Mandibulofacial dysostosis with alopecia results from ETAR gain-of-function mutations via allosteric effects on ligand binding

M. Ikeguchi, Y. Uchijima, Y. Kurihara, 2023, The Journal of clinical investigation.

Apo- and Antagonist-Binding Structures of Vitamin D Receptor Ligand-Binding Domain Revealed by Hybrid Approach Combining Small-Angle X-ray Scattering and Molecular Dynamics.

M. Ikeguchi, Toru Ekimoto, N. Shimizu, 2016, Journal of medicinal chemistry.

A synthetic ion channel with anisotropic ligand response

M. Ikeguchi, H. Noji, K. Kamagata, 2020, Nature Communications.

Elimination of Finite-Size Effects on Binding Free Energies via the Warp-Drive Method.

T. Yamane, M. Ikeguchi, Toru Ekimoto, 2018, Journal of chemical theory and computation.

Effect of Water Molecules on the Activating S810L Mutation of the Mineralocorticoid Receptor

Mitsunori Ikeguchi, Masateru Ohta, Toru Ekimoto, 2021, J. Chem. Inf. Model..

A theoretical framework for calculations of the structural relaxation time on the basis of the free energy landscape theory

T. Odagaki, Toru Ekimoto, Takashi Yoshidome, 2013 .

3D-RISM-AI: A Machine Learning Approach to Predict Protein–Ligand Binding Affinity Using 3D-RISM

T. Yamane, M. Ikeguchi, Toru Ekimoto, 2022, The journal of physical chemistry. B.

Structural basis for ligand recognition and signaling of hydroxy-carboxylic acid receptor 2

M. Ikeguchi, J. Tame, Toru Ekimoto, 2023, Nature communications.