計算構造生物学研究室

Structual Biology + Computer Science

研究実績

*Kota Kasahara, Hiroki Terazawa, Hayato Itaya, Satoshi Goto, Haruki Nakamura, Takuya Takahashi, Junichi
myPresto/omegagene 2020: a molecular dynamics simulation engine for virtual-system coupled sampling

2020Biophysics and Physicobiology17140-146doi: 10.2142/biophysico.BSJ-2020013 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

2020Journal of Chemical Information and Modeling60(10) 4767-4880doi: 10.1021/acs.jcim.0c00551 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 URL

Hayami,T., Higo,J., Nakamura,H. and Kasahara,K
Multidimensional virtual‐system coupled canonical molecular dynamics to compute free‐energy landscapes of peptide multimer assembly.

2019, J Comput Chem,10.1002/jcc.26020. 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 Volume 17, Pages 712-720 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, in press, doi: 10.1021/acs.jctc.8b01042 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, doi: 10.1371/journal.pone.0205052, 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.org/10.2142/biophysico.15.0_165, 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, doi: 10.7717/peerj.4769, 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, 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, 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, URL

Yoko Sugawara, Yuji Hiranoa, Shigefumi Yamamuraa, Shigeru Endo, Masanori Ootaki, Naoki Matsumoto and Takuya Takahashi,
Electrostatic energy of transfer and macrobond analyses of intermolecular interactions and hydration effects in protein crystals in a low ionic environment

2017, Journal of Crystal Growth, 468, 283-289, doi: 10.1016/j.jcrysgro.2016.09.072, URL

*Junichi Higo, Kota Kasahara, Haruki Nakamura,
Multi-dimensional virtual system introduced to enhance canonical sampling.

2017, The Journal of Chemical Physics, 147: 134102, doi: 10.1063/1.4986129, 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, none, 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, doi: 10.1371/journal.pone.0172654, 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, 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

Tetsuro Nagai, George A. Pantelopulos, Takuya Takahashi, John E. Straub,
On the use of mass scaling for stable and efficient simulated tempering with molecular dynamics

2016, J Computational Chemistry, 37/ 21, 2017–2028, doi:10.1002/jcc.24430, 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, doi: 10.1371/journal.pone.0167524, 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, URL

Kota Kasahara, *Kengo Kinoshita,
Landscape of protein-small ligand binding modes.

2016, Protein Science, 25(9):1659-71, doi: 10.1002/pro.2971, URL

*Kota Kasahara, Neetha Mohan, Ikuo Fukuda, Haruki Nakamura,
mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories

2016, Bioinformatics, 32(16):2531-3, doi: 10.1093/bioinformatics/btw129, 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, doi: 10.1371/journal.pone.0150716, URL

Tetsuro Nagai and Takuya Takahashi,
Momentum and Velocity Scaling Rules in Replica-Exchange Molecular Dynamics Simulations with Mass Manipulation

2015, JPS Conf. Proc., 11009.0, 10.7566/JPSCP.5.011009, URL

Nagai T1, Takahashi T1.,
Mass-scaling replica-exchange molecular dynamics optimizes computational resources with simpler algorithm.

2014, J Chem Phys., 141/ 11, 11411, doi:10.1063/1.4895510, URL

Hiromichi Tsurui, Takuya Takahashi, Yuko Matsuda, Qingshun Lin, Aya Sato-Hayashizaki,and Sachiko Hirose,
Exhaustive Characterization of TCR–pMHC Binding Energy Estimated by the String Model and Miyazawa-Jernigan Matrix

2013, General Medicine, 2327-5146, doi:10.3109/14397595.2014.950035, URL

Hiroko Fukano,† Takuya Takahashi,‡ Mamoru Aizawa,§ and Hideyuki Yoshimura,
Synthesis of Uniform and Dispersive Calcium Carbonate Nanoparticles in a Protein Cage through Control of Electrostatic Potential

2011, Inorganic Chemistry, 50/ 14, 6526–6532, doi:10.1021/ic200117x, URL

Ikuo Kurisakia, Takuya Takahashi,
Assessment of dynamic properties of water around a monovalent ion: A classical molecular dynamics simulation study

2011, Computational and Theoretical Chemistry, 966/ 1-3, 26-30, doi:10.1016, URL

Masanori Ootaki, Shigeru Endo, Yoko Sugawara and Takuya Takahashi,
Crystal Habits of Cubic Insulin and Evaluation of Intermolecular Interactions by Macrobond and EET Analyses

2009, Journal of Crystal Growth, 311/ 17, 4226-4234, , URL

Motoi Yamashita and Takuya Takahashi,
Melt Crystallization of isotactic Polybutene-1Trigonal Form: the Effect of Side Chain Entropy on Crystal Growth Kinetics

2008, Polymer Journal , 140/ 10, 1010-1016, , URL

Motoi Yamashita and Takuya Takahashi,
Kinetic Roughening Transition of isotactic Polybutene-1 Tetragonal Crystals: Disagreement between Morphology and Growth Kinetics

2008, Polymer Journal, 140/ 10, 1005-1009, , URL

Motoi Yamashita and Takuya Takahashi,
Directional Entropy of Chain Folding Detected in Chain Folding Free Energies? Crystal Thickness Transition of isotactic Polybutene-1 Tetragonal Phase

2008, Polymer Journal, 140/ 10, 996-1004, , URL

Masanori Ootaki, Shigeru Endo, Yoko Sugawara, Takuya Takahashi, and Nakasako Masayoshi,
Investigation of morphology and surface microtopograph of cubic insulin

2008, Acta Crystallography, 64, 582-582, , URL

山下基 髙橋卓也,
高分子側鎖のエントロピーが結晶表面に与える影響:ポリブテン正方晶と三方晶の表面自由エネルギー

2008, 高分子論文集, 65/ 3, 218-227, , URL

Takuya Takahashi,
Calculation of Electrostatic Solvation Free Energy of Protein Molecules: Size Dependence and Error Evaluation of the Calculation Method

2008, Memoirs of the Institute of Science & Engineering, , , URL

Hiromichi Tsurui and Takuya Takahashi,
Prediction of T-Cell Epitope

2007, Journal of Pharmacological Sciences, 105/ 4, 299-316, , URL

Motoi Yamashita and Takuya Takahashi,
Morphological Transition of Isotactic Polybutene-1 Tetragonal Crystals: Optical and Transmission Electron Microscopy Observation

2007, Modern Research and Educational Topics in Microscopy, 2, 713-718, , URL

Wataru Nemotoa, Takashi Imai, Takuya Takahashi, Takeshi Kikuchic, and Norihisa Fujita,
Detection of pairwise residue proximity by covariation analysis for 3D-structure prediction of G-protein-coupled receptors

2004, The Protein Journal, 23/ 6, 427-435, 10.1023/B:JOPC.0000039556.95629.cf, URL

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