Kota Kasahara
Kota Kasahara
College of Life Sciences, Ritsumeikan University
Verified email at - Homepage
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ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants
T Obayashi, K Nishida, K Kasahara, K Kinoshita
Plant and cell physiology 52 (2), 213-219, 2011
A novel approach of dynamic cross correlation analysis on molecular dynamics simulations and its application to Ets1 dimer–DNA complex
K Kasahara, I Fukuda, H Nakamura
PloS one 9 (11), e112419, 2014
Virtual‐system‐coupled adaptive umbrella sampling to compute free‐energy landscape for flexible molecular docking
J Higo, B Dasgupta, T Mashimo, K Kasahara, Y Fukunishi, H Nakamura
Journal of Computational Chemistry 36 (20), 1489-1501, 2015
Studies on molecular dynamics of intrinsically disordered proteins and their fuzzy complexes: A mini-review
K Kasahara, H Terazawa, T Takahashi, J Higo
Computational and structural biotechnology journal 17, 712-720, 2019
Phosphorylation of an intrinsically disordered region of Ets1 shifts a multi-modal interaction ensemble to an auto-inhibitory state
K Kasahara, M Shiina, J Higo, K Ogata, H Nakamura
Nucleic acids research 46 (5), 2243-2251, 2018
Tight-binding quantum chemical molecular dynamics study on first proton transfer process of ORR catalyzed by cobalt-porphyrin complex
K Kasahara, H Tsuboi, M Koyama, A Endou, M Kubo, CA Del Carpio, ...
Electrochemical and solid-state letters 9 (11), A490, 2006
myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme
K Kasahara, B Ma, K Goto, B Dasgupta, J Higo, I Fukuda, T Mashimo, ...
Biophysics and physicobiology 13, 209-216, 2016
Ligand-binding site prediction of proteins based on known fragment–fragment interactions
K Kasahara, K Kinoshita, T Takagi
Bioinformatics 26 (12), 1493-1499, 2010
Comprehensive classification and diversity assessment of atomic contacts in protein–small ligand interactions
K Kasahara, M Shirota, K Kinoshita
Journal of chemical information and modeling 53 (1), 241-248, 2013
GIANT: pattern analysis of molecular interactions in 3D structures of protein–small ligand complexes
K Kasahara, K Kinoshita
BMC bioinformatics 15 (1), 1-6, 2014
Enhanced sampling of molecular dynamics simulations of a polyalanine octapeptide: effects of the periodic boundary conditions on peptide conformation
K Kasahara, S Sakuraba, I Fukuda
The Journal of Physical Chemistry B 122 (9), 2495-2503, 2018
Ion concentration-dependent ion conduction mechanism of a voltage-sensitive potassium channel
K Kasahara, M Shirota, K Kinoshita
PLoS One 8 (2), e56342, 2013
Architecture of an FPGA accelerator for molecular dynamics simulation using OpenCL
HM Waidyasooriya, M Hariyama, K Kasahara
2016 IEEE/ACIS 15th International Conference on Computer and Information …, 2016
New protocol for predicting the ligand-binding site and mode based on the 3D-RISM/KH theory
M Sugita, M Hamano, K Kasahara, T Kikuchi, F Hirata
Journal of Chemical Theory and Computation 16 (4), 2864-2876, 2020
Multimodal structural distribution of the p53 C-terminal domain upon binding to S100B via a generalized ensemble method: from disorder to extradisorder
S Iida, T Kawabata, K Kasahara, H Nakamura, J Higo
Journal of Chemical Theory and Computation 15 (4), 2597-2607, 2019
Enhancement of canonical sampling by virtual-state transitions
J Higo, K Kasahara, B Dasgupta, H Nakamura
The Journal of Chemical Physics 146 (4), 044104, 2017
Free-energy landscape of molecular interactions between endothelin 1 and human endothelin type B receptor: fly-casting mechanism
J Higo, K Kasahara, M Wada, B Dasgupta, N Kamiya, T Hayami, I Fukuda, ...
Protein Engineering, Design and Selection 32 (7), 297-308, 2019
An FPGA Accelerator for Molecular Dynamics Simulation Using OpenCL.
HM Waidyasooriya, M Hariyama, K Kasahara
Int. J. Networked Distributed Comput. 5 (1), 52-61, 2017
Multidimensional virtual‐system coupled canonical molecular dynamics to compute free‐energy landscapes of peptide multimer assembly
T Hayami, J Higo, H Nakamura, K Kasahara
Journal of Computational Chemistry 40 (28), 2453-2463, 2019
Multi-dimensional virtual system introduced to enhance canonical sampling
J Higo, K Kasahara, H Nakamura
The Journal of Chemical Physics 147 (13), 134102, 2017
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