| Kota Kasahara, Hideyuki Tsuboi, Michihisa Koyama, Akira Endou, Momoji Kubo, Calros Adriel Del Carpio, *Akira Miyamoto |
"Tight-Binding Quantum Chemical Molecular Dynamics Study on First Proton Transfer Process of ORR Catalyzed by Cobalt-Porphyrin Complex." |
2006 |
Electrochemical and Solid State Letters |
9 |
A490-A493 |
doi: 10.1149/1.2336985 |
URL |
| *Kota Kasahara, Kengo Kinoshita, Toshihisa Takagi |
"Ligand-binding site prediction of proteins based on known fragment-fragment interactions." |
2010 |
Bioinformatics |
26(12) |
1493-1499 |
doi: 10.1093/bioinformatics/btq232 |
PubMed |
URL |
| *Takeshi Obayashi, Kozo Nishida, Kota Kasahara, Kengo Kinoshita |
"ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants." |
2011 |
Plant and Cell Physiology |
52 |
213-219 |
doi: 10.1093/pcp/pcq203 |
PubMed |
URL |
| Kota Kasahara, Matsuyuki Shirota, *Kengo Kinoshita |
"Comprehensive classification and diversity assessment of atomic contacts in protein-small ligand interactions." |
2013 |
Journal of Chemical Information and Modeling |
53(1) |
241-248 |
doi: 10.1021/ci300377f |
PubMed |
URL |
| Kota Kasahara, Matsuyuki Shirota, *Kengo Kinoshita |
"Ion Concentration-Dependent Ion Conduction Mechanism of a Voltage-Sensitive Potassium Channel." |
2013 |
PLoS ONE |
8:e56342 |
1-8 |
doi: 10.1371/journal.pone.0056342 |
PubMed |
URL |
| Kota Kasahara, *Kengo Kinoshita |
"GIANT: pattern analysis of molecular interactions in 3D structures of protein–small ligand complexes." |
2014 |
BMC Bioinformatics |
15:12 |
1-6 |
doi: 10.1186/1471-2105-15-12 |
PubMed |
URL |
| Bhaskar Dasgupta, Kota Kasahara, Narutoshi Kamiya, Haruki Nakamura, *Akira R Kinjo |
"ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants." |
2014 |
PLoS ONE |
9:e91347 |
1-16 |
do+I6i: 10.1371/journal.pone.0091347 |
PubMed |
URL |
| *Kota Kasahara, Ikuo Fukuda, Haruki Nakamura |
"A Novel Approach of Dynamic Cross Correlation Analysis on Molecular Dynamics Simulations and Its Application to Ets1 Dimer-DNA Complex." |
2014 |
PLoS ONE |
9(11):e112419 |
1-13 |
doi: 10.1371/journal.pone.0112419 |
PubMed |
URL |
| *Junichi Higo, Bhaskar Dasgupta, Tadaaki Mashimo, Kota Kasahara, Yoshifumi Fukunishi, Haruki Nakamura |
"Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking." |
2015 |
Journal of Computational Chemistry |
36(20) |
1489-1501 |
doi: 10.1002/jcc.23948 |
PubMed |
URL |
| Kota Kasahara, Matsuyuki Shirota, *Kengo Kinoshita |
"Ion Concentration- and Voltage-Dependent Push and Pull Mechanisms of Potassium Channel Ion Conduction" |
2016 |
PLoS ONE |
11:e0150716 |
1-15 |
doi: 10.1371/journal.pone.0150716 |
PubMed |
URL |
| *Kota Kasahara, Neetha Mohan, Ikuo Fukuda, Haruki Nakamura |
"mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories" |
2016 |
Bioinformatics |
32(16) |
2531-2533 |
doi: 10.1093/bioinformatics/btw129 |
PubMed |
URL |
| *Kota Kasahara, Kengo Kinoshita |
"Landscape of protein-small ligand binding modes." |
2016 |
Protein Science |
25(9) |
1659-1671 |
doi: 10.1002/pro.2971 |
PubMed |
URL |
| *Kota Kasahara, Benson Ma, Kota Goto, Bhaskar Dasgupta, Junichi Higo, Ikuo Fukuda, Tadaaki Mashimo, Yutaka Akiyama, Haruki Nakamura |
"myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme" |
2016 |
Biophysics and Physicobiology |
13 |
209-216 |
doi: 10.2142/biophysico.13.0_209 |
PubMed |
URL |
| *Kota Kasahara, Kengo Kinoshita |
"IBiSA_tools: A Computational Toolkit for Ion-binding State Analysis in Molecular Dynamics Trajectories of Ion Channels " |
2016 |
PLoS ONE |
11(12): e0167524 |
1-9 |
doi: 10.1371/journal.pone.0167524 |
PubMed |
URL |
| Hasitha Muthumala Waidyasooriya, Masanori Hariyama, Kota Kasahara |
"An FPGA Accelerator for Molecular Dynamics Simulation Using OpenCL" |
2017 |
International Journal of Networked and Distributed Computing |
5(1) |
52-61 |
doi: 10.1109/ICIS.2016.7550743 |
URL |
| *Junichi Higo, Kota Kasahara, Bhaskar Dasgupta, Haruki Nakamura |
"Enhancement of canonical sampling by virtual-state transitions" |
2017 |
The Journal of Chemical Physics |
146: 044104 |
1-12 |
doi: 10.1063/1.4974087 |
PubMed |
URL |
| *Kota Kasahara, Masaaki Shiina, Ikuo Fukuda, Kazuhiro Ogata, Haruki Nakamura |
"Molecular mechanisms of cooperative binding of transcription factors Runx1–CBFβ–Ets1 on the TCRα gene enhancer." |
2017 |
PLoS ONE |
12(2): e0172654 |
1-18 |
doi:10.1371/journal.pone.0172654 |
PubMed |
URL |
| Hasitha Muthumala Waidyasooriya, Masanori Hariyama, Kota Kasahara |
"OpenCL-Based Implementation of an FPGA Accelerator for Molecular Dynamics Simulation." |
2017 |
Information Engineering Express |
3(2) |
11-23 |
|
URL |
| *Junichi Higo, Kota Kasahara, Haruki Nakamura |
"Multi-dimensional virtual system introduced to enhance canonical sampling." |
2017 |
The Journal of Chemical Physics |
147: 134102 |
1-13 |
doi: 10.1063/1.4986129 |
PubMed |
URL |
| *Kota Kasahara, Shun Sakuraba, Ikuo Fukuda |
"Enhanced Sampling of Molecular Dynamics Simulations of a Polyalanine Octapeptide: Effects of the Periodic Boundary Conditions on Peptide Conformation" |
2018 |
The Journal of Physical Chemistry B |
122(9) |
2495-2503 |
doi: 10.1021/acs.jpcb.7b10830 |
PubMed |
URL |
| *†Kota Kasahara, *†Masaaki Shiina, Junichi Higo, Kazuhiro Ogata, Haruki Nakamura |
"Phosphorylation of an intrinsically disordered region of Ets1 shifts a multi-modal interaction ensemble to an auto-inhibitory state." |
2018 |
Nucleic Acids Research |
46(5) |
2243-2251 |
doi: 10.1093/nar/gkx1297 |
PubMed |
URL |
| †Naoki Ogasawara, *†Kota Kasahara, Ryosuke Iwai, Takuya Takahashi |
"Unfolding of α-helical 20-residue poly-glutamic acid analyzed by multiple runs of canonical molecular dynamics simulations" |
2018 |
PeerJ |
6:e4769 |
1-17 |
doi: 10.7717/peerj.4769 |
PubMed |
URL |
| Tomonori Hayami, Kota Kasahara, Haruki Nakamura, *Junichi Higo |
"Molecular Dynamics Coupled with a Virtual System for Effective Conformational Sampling" |
2018 |
Journal of Computational Chemistry |
39(19) |
1291-1299 |
doi: 10.1002/jcc.25196 |
PubMed |
URL |
| †Ryosuke Iwai, *†Kota Kasahara, Takuya Takahashi |
"Influence of various parameters in the replica-exchange molecular dynamics method: Number of replicas, replica-exchange frequency, and thermostat coupling time constant" |
2018 |
Biophysics and Physicobiology |
15 |
165-172 |
doi: 10.2142/biophysico.15.0_165 |
PubMed |
URL |
| *Kota Kasahara, Shintaro Minami, Yasunori Aizawa |
"Characteristics of interactions at protein segments without non-local intramolecular contacts in the Protein Data Bank" |
2018 |
PLoS ONE |
13(12): e0205052. |
1-14 |
doi: 10.1371/journal.pone.0205052 |
PubMed |
URL |
| Shinji Iida, Takeshi Kawabata, Kota Kasahara, Haruki Nakamura, *Junichi Higo |
"Multimodal Structural Distribution of the p53 C-Terminal Domain upon Binding to S100B via a Generalized Ensemble Method: From Disorder to Extradisorder" |
2019 |
Journal of Chemical Theory and Computation |
15(4) |
2597-2607 |
doi: 10.1021/acs.jctc.8b01042 |
PubMed |
URL |
| *Kota Kasahara, Hiroki Terazawa, Takuya Takahashi, Junichi Higo |
"Studies on molecular dynamics of intrinsically disordered proteins and their fuzzy complexes: A mini-review" |
2019 |
Computational and Structural Biotechnology Journal |
17 |
712-720 |
doi: 10.1016/j.csbj.2019.06.009 |
PubMed |
URL |
| Tomonori Hayami, Junichi Higo, Haruki Nakamura, *Kota Kasahara |
"Multidimensional virtual-system coupled canonical molecular dynamics to compute free-energy landscapes of peptide multimer assembly" |
2019 |
Journal of Computational Chemistry |
40(28) |
2453-2463 |
doi: 10.1002/jcc.26020 |
PubMed |
URL |
| Yusuke Nomoto, Yukihiro Kubota, Yuto Ohnishi, Kota Kasahara, Aimi Tomita, Takehiro Oshime, Hiroki Yamashita, Muhamad Fahmi, *Masahiro Ito |
"Gene Cascade Finder: A tool for identification of gene cascades and its application in Caenorhabditis elegans" |
2019 |
PLoS ONE |
14(9):e0215187 |
1–16 |
doi: 10.1371/journal.pone.0215187 |
PubMed |
URL |
| †Takuya Shimato, *†Kota Kasahara, Junichi Higo, Takuya Takahashi |
"Effects of number of parallel runs and frequency of bias-strength replacement in generalized ensemble molecular dynamics simulations." |
2019 |
PeerJ Physical Chemistry |
1:e4 |
1–20 |
doi: 10.7717/peerj-pchem.4 |
URL |
| *Junichi Higo, Kota Kasahara, Mitsuhito Wada, Bhaskar Dasgupta, Narutoshi Kamiya, Tomonori Hayami, Ikuo Fukuda, Yoshifumi Fukunishi, *Haruki Nakamura |
"Free-energy landscape of molecular interactions between endothelin 1 and human endothelin type B receptor: Fly-casting mechanism" |
2019 |
Protein Engineering, Design and Selection |
32(7) |
297–308 |
doi: 10.1093/protein/gzz029 |
PubMed |
URL |
| *Kota Kasahara, Yuki Takimoto, Ryoi Ashida, Takuya Takahashi |
"Effects of ion–water Lennard-Jones potentials on the hydration dynamics around a monovalent atomic ion in molecular dynamics simulations." |
2020 |
Molecular Simulation |
46(2) |
83-91 |
doi: 10.1080/08927022.2019.1675883 |
URL |
| *Masatake Sugita, Masataka Hamano, Kota Kasahara, Takeshi Kikuchi, Fumio Hirata |
"New Protocol for Predicting the Ligand-Binding Site and Mode Based on the 3D-RISM/KH Theory" |
2020 |
Journal of Chemical Theory and Computation |
16(4) |
2864–2876 |
doi: 10.1021/acs.jctc.9b01069 |
PubMed |
URL |
| *Junichi Higo, Takeshi Kawabata, Ayumi Kusaka, Kota Kasahara, Narutoshi Kamiya, Ikuo Fukuda, Kentaro Mori, Yutaka Hata, Yoshifumi Fukunishi, Haruki Nakamura |
"Molecular interaction mechanism of a 14-3-3 protein with a phosphorylated peptide elucidated by enhanced conformational sampling" |
2020 |
Journal of Chemical Information and Modeling |
60(10) |
4767-4880 |
doi: 10.1021/acs.jcim.0c00551 |
PubMed |
URL |
| *Kota Kasahara, Hiroki Terazawa, Hayato Itaya, Satoshi Goto, Haruki Nakamura, Takuya Takahashi, Junichi Higo |
"myPresto/omegagene 2020: a molecular dynamics simulation engine for virtual-system coupled sampling" |
2020 |
Biophysics and Physicobiology |
17 |
140-146 |
doi: 10.2142/biophysico.BSJ-2020013 |
PubMed |
URL |
| *Junichi Higo, Ayumi Kusaka, Kota Kasahara, Narutoshi Kamiya, Itaya Hayato, Xie Qilin, Takuya Takahashi, Ikuo Fukuda, Kentaro Mori, Yutaka Hata, Yoshifumi Fukunishi |
"GA-guided mD-VcMD: A genetic-algorithm-guided method for multi-dimensional virtual-system coupled molecular dynamics" |
2020 |
Biophysics and Physicobiology |
17 |
161-176 |
doi: 10.2142/biophysico.BSJ-2020008 |
PubMed |
URL |
| Tomonori Hayami, Narutoshi Kamiya, *Kota Kasahara, Takeshi Kawabata, Jun-ichi Kurita, Yoshifumi Fukunishi, Yoshifumi Nishimura, Haruki Nakamura, *Junichi Higo |
"Difference of binding modes among three ligands to a receptor mSin3B corresponding to their inhibitory activities" |
2021 |
Scientific Reports |
11 |
6178 |
doi: 10.21203/rs.3.rs-139177 |
PubMed |
URL |
| Hayato Itaya, *Kota Kasahara, Qilin Xie, Yoshiaki Yano, Katsumi Matsuzaki, Takuya Takahashi |
"All-Atom Molecular Dynamics Elucidating Molecular Mechanisms of Single-Transmembrane Model Peptide Dimerization in a Lipid Bilayer" |
2021 |
ACS Omega |
6(17) |
11458–11465 |
doi: 10.1021/acsomega.1c00482 |
PubMed |
URL |
| *Shun Sakuraba, Qilin Xie, Kota Kasahara, Junichi Iwakiri, Hidetoshi Kono |
"Extended ensemble simulations of a SARS-CoV-2 nsp1-5'-UTR complex" |
2022 |
PLoS Computational Biology |
18(1) |
e1009804 |
doi: 10.1371/journal.pcbi.1009804 |
PubMed |
URL |
| Ryohei Kondo, *Kota Kasahara, Takuya Takahashi |
"Information quantity for secondary structure propensities of protein subsequences in the Protein Data Bank" |
2022 |
Biophysics and Physicobiology |
19 |
e190002 |
doi: 10.2142/biophysico.bppb-v19.0002 |
PubMed |
URL |
| Tomomi Ukawa, Fumihiko Banno, Toshiki Ishikawa, Kota Kasahara, Yuuta Nishina, Rika Inoue, Keigo Tsujii, Masatoshi Yamaguchi, Takuya Takahashi, Yoichiro Fukao, Maki Kawai-Yamada, Minoru Nagano |
"Sphingolipids with 2-hydroxy fatty acids aid in plasma membrane nanodomain organization and oxidative burst" |
2022 |
Plant Physiology |
189(2) |
839-857 |
doi: 10.1093/plphys/kiac134 |
PubMed |
URL |
| Junichi Higo, Kota Kasahara, Gert-Jan Bekker, Benson Ma, Shun Sakuraba, Shinji Iida, Narutoshi Kamiya, Ikuo Fukuda, Hidetoshi Kono, Yoshifumi Fukunishi, Haruki Nakamura |
"Fly casting with ligand sliding and orientational selection supporting complex formation of a GPCR and a middle sized flexible molecule" |
2022 |
Scientific Reports |
12(1) |
13792 |
doi: 10.1038/s41598-022-17920-7 |
PubMed |
URL |
| *Yoshifumi Fukunishi, Junichi Higo, Kota Kasahara |
"Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles" |
2022 |
Biophysical Reviews |
|
|
doi: 10.1007/s12551-022-01015-8 |
PubMed |
URL |
| Toru Sengoku, Masaaki Shiina, Kae Suzuki, Keisuke Hamada, Ko Sato, Akiko Uchiyama, Shunsuke Kobayashi, Asako Oguni, Hayato Itaya, Kota Kasahara, Hirotomo Moriwaki, Chiduru Watanabe, Teruki Honma, Chikako Okada, Shiho Baba, Tsutomu Ohta, Hozumi Motohashi, Masayuki Yamamoto, Kazuhiro Ogata |
"Structural basis of transcription regulation by CNC family transcription factor, Nrf2" |
2022 |
Nucleic Acids Research |
50(21) |
12543–12557 |
doi: 10.1093/nar/gkac1102 |
PubMed |
URL |
