Research accomplishments - Koda Shin-ichi

dmf-g16: A Gaussian Wrapper for Reliable Double-Ended Transition-State Searches with Native Input Formats

2026.01.27

DOI

Osimertinib’s Proton-Catalyzed, Pseudoconcerted EGFR Inhibition Guides Next-Generation Inhibitor Design

Journal of Chemical Information and Modeling    2026.01.26

DOI

General and scalable atom-to-atom mapping via Weisfeiler–Lehman-like approximate graph matching

2025.11.24

DOI

Correlated Flat-Bottom Elastic Network Model for Improved Bond Rearrangement in Reaction Paths

Journal of Chemical Theory and Computation    2025.04.08

DOI

Flat-Bottom Elastic Network Model for Generating Improved Plausible Reaction Paths

Journal of Chemical Theory and Computation    2024.08.16

DOI

A Correlated Flat-bottom Elastic Network Model for Improved Bond Rearrangement in Reaction Paths

2024.07.22

DOI

A Correlated Flat-bottom Elastic Network Model for Improved Bond Rearrangement in Reaction Paths

2024.07.11

DOI

A Flat-bottom Elastic Network Model for Generating Improved Plausible Reaction Paths

ChemRxiv    2024

ISSN: 25732293

DOI

Locating Transition States by Variational Reaction Path Optimization with an Energy-Derivative-Free Objective Function

Journal of Chemical Theory and Computation    2024

ISSN: 15499626 15499618

DOI

Multimeric structure enables the acceleration of KaiB-KaiC complex formation induced by ADP/ATP exchange inhibition

PLoS Computational Biology    2022

ISSN: 15537358 1553734X

DOI

Regulation mechanisms of the dual ATPase in KaiC

Proceedings of the National Academy of Sciences of the United States of America    2022

ISSN: 10916490 00278424

DOI

Regulation mechanisms of the dual ATPase in KaiC

bioRxiv    2021

ISSN: 26928205

DOI

Ring-shaped multimeric structure enables the acceleration of KaiB-KaiC complex formation induced by the ADP/ATP exchange inhibition

bioRxiv    2021

ISSN: 26928205

DOI

An alternative interpretation of the slow KaiB-KaiC binding of the cyanobacterial clock proteins

bioRxiv    2020

ISSN: 26928205

DOI

An alternative interpretation of the slow KaiB-KaiC binding of the cyanobacterial clock proteins

Scientific Reports    2020

ISSN: 20452322

DOI

Author Correction: Conformational rearrangements of the C1 ring in KaiC measure the timing of assembly with KaiB (Scientific Reports, (2018), 8, 1, (8803), 10.1038/s41598-018-27131-8)

Scientific Reports    2020

ISSN: 20452322

DOI

Molecular mechanism of acceleration and retardation of collective orientation relaxation of water molecules in aqueous solutions

Journal of Physical Chemistry B    2020

ISSN: 15205207 15206106

DOI

Sufficiency of unidirectional allostery in KaiC in generating the cyanobacterial circadian rhythm

bioRxiv    2020

ISSN: 26928205

DOI

Conformational rearrangements of the C1 ring in KaiC measure the timing of assembly with KaiB

Scientific Reports    2018.12

ISSN: 2045-2322

DOI

Mixed semiclassical-classical propagators for the Wigner phase space representation

The Journal of Chemical Physics    2016.04.21

DOI