| 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 | 180 | 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 | 115 | 2014 |
| 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 | 40 | 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 | 37 | 2018 |
| 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 | 32 | 2016 |
| 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 | 30 | 2015 |
| 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 | 24 | 2006 |
| Ligand-binding site prediction of proteins based on known fragment–fragment interactions K Kasahara, K Kinoshita, T Takagi Bioinformatics 26 (12), 1493-1499, 2010 | 21 | 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 | 19 | 2013 |
| 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 | 18 | 2018 |
| 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 | 16 | 2020 |
| GIANT: pattern analysis of molecular interactions in 3D structures of protein–small ligand complexes K Kasahara, K Kinoshita BMC bioinformatics 15, 1-6, 2014 | 16 | 2014 |
| 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 | 15 | 2019 |
| 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 | 15 | 2016 |
| Structural basis of transcription regulation by CNC family transcription factor, Nrf2 T Sengoku, M Shiina, K Suzuki, K Hamada, K Sato, A Uchiyama, ... Nucleic acids research 50 (21), 12543-12557, 2022 | 14 | 2022 |
| 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 | 14 | 2019 |
| Ion concentration-dependent ion conduction mechanism of a voltage-sensitive potassium channel K Kasahara, M Shirota, K Kinoshita PLoS One 8 (2), e56342, 2013 | 14 | 2013 |
| 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 | 13 | 2019 |
| Enhancement of canonical sampling by virtual-state transitions J Higo, K Kasahara, B Dasgupta, H Nakamura The Journal of Chemical Physics 146 (4), 2017 | 12 | 2017 |
| Molecular mechanisms of cooperative binding of transcription factors Runx1–CBFβ–Ets1 on the TCRα gene enhancer K Kasahara, M Shiina, I Fukuda, K Ogata, H Nakamura PLoS One 12 (2), e0172654, 2017 | 11 | 2017 |
