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List of works by Kota Kasahara

ATTED-II Updates: Condition-Specific Gene Coexpression to Extend Coexpression Analyses and Applications to a Broad Range of Flowering Plants ⬇️

scientific article published on January 7, 2011

Characteristics of interactions at protein segments without non-local intramolecular contacts in the Protein Data Bank ⬇️

scientific article published in PLoS ONE

Comprehensive classification and diversity assessment of atomic contacts in protein-small ligand interactions

scientific article published on 18 December 2012

Enhanced Sampling of Molecular Dynamics Simulations of a Polyalanine Octapeptide: Effects of the Periodic Boundary Conditions on Peptide Conformation.

scientific article published on 13 February 2018

Enhancement of canonical sampling by virtual-state transitions.

scientific article

Extended ensemble simulations of a SARS-CoV-2 nsp1-5'-UTR complex

scientific article published on 19 January 2022

GIANT: pattern analysis of molecular interactions in 3D structures of protein-small ligand complexes.

scientific article published on 14 January 2014

IBiSA_Tools: A Computational Toolkit for Ion-Binding State Analysis in Molecular Dynamics Trajectories of Ion Channels

scientific article

Ion Concentration- and Voltage-Dependent Push and Pull Mechanisms of Potassium Channel Ion Conduction

scientific article (publication date: 2016)

Ion concentration-dependent ion conduction mechanism of a voltage-sensitive potassium channel

scientific article (publication date: 2013)

Landscape of protein-small ligand binding modes

scientific article published on 21 June 2016

Ligand-binding site prediction of proteins based on known fragment-fragment interactions.

scientific article

Molecular dynamics coupled with a virtual system for effective conformational sampling

scientific article published on 21 February 2018

Multi-dimensional virtual system introduced to enhance canonical sampling

scientific article published in October 2017

Multidimensional virtual-system coupled canonical molecular dynamics to compute free-energy landscapes of peptide multimer assembly

scientific article published on 07 July 2019

Multimodal Structural Distribution of the p53 C-Terminal Domain upon Binding to S100B via a Generalized Ensemble Method: From Disorder to Extradisorder

scientific article published on 22 March 2019

New Protocol for Predicting the Ligand-Binding Site and Mode Based on the 3D-RISM/KH Theory

scientific article published on 27 March 2020

Unfolding of α-helical 20-residue poly-glutamic acid analyzed by multiple runs of canonical molecular dynamics simulations.

scientific article published on 15 May 2018

Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking

scientific article published on 4 June 2015

mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories

scientific article

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