Kamiya Narutoshi 神谷成敏

… Alternative Names

KAMIYA Narutoshi 神谷成敏

神谷成敏カミヤナルトシ

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Researcher Number	80420462
Other IDs	https://orcid.org/0000-0002-0527-6968
Affiliation (Current)	2025: 兵庫県立大学, 情報科学研究科, 特任教授
Affiliation (based on the past Project Information) *help	2025: 兵庫県立大学, 情報科学研究科, 特任教授 2020 – 2023: 兵庫県立大学, 情報科学研究科, 特任教授 2021: 兵庫県立大学, 情報科学研究科, 客員教授 2016 – 2018: 兵庫県立大学, シミュレーション学研究科, 特任教授 2015: 国立研究開発法人理化学研究所, 計算科学研究機構, 研究員 … More 2012 – 2014: 大阪大学, たんぱく質研究所, 招へい研究員 2013: 大阪大学, たんぱく質研究所, 特任研究員 2012: 大阪大学, 蛋白質研究所, 招へい研究員 2010 – 2011: 大阪大学, 蛋白質研究所, 特任研究員 2010: 大阪大学, 蛋白質研究所, 特任研究員(客員准教授) 2007: 大阪大学, 臨床医工学融合研究教育センター, 特任研究員 2005: 神戸大学, 大学院・医学系研究科, 科学技術研究員 Less
Review Section/Research Field	Principal Investigator Biophysics / Basic Section 43040:Biophysics-related Except Principal Investigator Biophysics / Biological Sciences / Basic Section 38030:Applied biochemistry-related / Biological Sciences
Keywords	Principal Investigator 分子動力学シミュレーション / 構造予測 / 自由エネルギー / 親和性予測 / 生物物理 / 立体構造予測 / 抗原抗体 / 構造・機能予測 / 機能予測 / 構造 … More Except Principal Investigator … More 生体分子 / 蛋白質 / 生物物理 / 蛋白質間相互作用 / プロテオーム / 分子シミュレーション / 分子動力学 / 動的構造変化 / 金属イオン結合 / 構造機能相関 / PET分解 / 酵素 / ヌクレオソーム / ポリメラーゼ / 生体生命情報学 / 分子動力学計算 / 遺伝子 / 転写因子 / 構造・機能予測 / データベース / バイオインフォマティクス / 蛋白質の構造・機能予測 / 分子軌道法 / 分子動力学法 / 密度汎関数法 / モノアミン酸化酵素A / チトクロムc酸化酵素 / 生体超分子複合体 / 量子化学 / 酵素反応 Less

T細胞受容体に対するデータ駆動型分子デザイン法の開発Principal Investigator
- Principal Investigator
  
  神谷成敏
- Project Period (FY)
  2025 – 2027
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Review Section
  
  Basic Section 43040:Biophysics-related
- Research Institution
  University of Hyogo
Structural dynamics of cutinase Cut190 upon Ca2+ binding and molecular mechanism of PET degradation by Cut190
- Principal Investigator
  
  Oda Masayuki
- Project Period (FY)
  2021 – 2023
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 38030:Applied biochemistry-related
- Research Institution
  Kyoto Prefectural University
Complex structure and affinity prediction among cancer vaccine peptides and immune related proteinsPrincipal Investigator
- Principal Investigator
  
  Kamiya Narutoshi
- Project Period (FY)
  2020 – 2022
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 43040:Biophysics-related
- Research Institution
  University of Hyogo
Accurate predictions of complex structure and affinity between proteins and drugsPrincipal Investigator
- Principal Investigator
  
  Kamiya Narutoshi
- Project Period (FY)
  2016 – 2018
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Research Field
  
  Biophysics
- Research Institution
  University of Hyogo
Development of a complex structure prediction method between proteins using binding free-energy as a scoring functionPrincipal Investigator
- Principal Investigator
  
  Kamiya Narutoshi
- Project Period (FY)
  2013 – 2015
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Research Field
  
  Biophysics
- Research Institution
  Institute of Physical and Chemical Research
  Osaka University
Elucidation of information-processing mechanisms during transcription cycle using computational and information sciences
- Principal Investigator
  
  NAKAMURA Haruki
- Project Period (FY)
  2012 – 2016
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Review Section
  
  Biological Sciences
- Research Institution
  Osaka University
Quantitative computational and informatics studies on protein-protein interaction systems based on their dynamic structures
- Principal Investigator
  
  NAKAMURA Haruki
- Project Period (FY)
  2011 – 2013
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Research Field
  
  Biophysics
- Research Institution
  Osaka University
Development of the free-energy evaluation method between protein and drug moleculesPrincipal Investigator
- Principal Investigator
  
  KAMIYA Narutoshi
- Project Period (FY)
  2010 – 2012
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Research Field
  
  Biophysics
- Research Institution
  Osaka University
Structural Interactome Studies from Computational and Bioinformatics Approaches
- Principal Investigator
  
  NAKAMURA Haruki
- Project Period (FY)
  2008 – 2010
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Research Field
  
  Biophysics
- Research Institution
  Osaka University
分子シミュレーション支援による生体超分子複合体の構造機能相関の理論的研究
- Principal Investigator
  
  鷹野優
- Project Period (FY)
  2006 – 2007
- Research Category
  
  Grant-in-Aid for Scientific Research on Priority Areas
- Review Section
  
  Biological Sciences
- Research Institution
  Osaka University
分子シミュレーション支援による生体超分子複合体の構造・機能解析
- Principal Investigator
  
  NAKAMURA Haruki
- Project Period (FY)
  2005
- Research Category
  
  Grant-in-Aid for Scientific Research on Priority Areas
- Review Section
  
  Biological Sciences
- Research Institution
  Osaka University

[Book] タンパク質計算科学2009
- Author(s)
  神谷成敏・肥後順一・福西快文・中村春木
- Total Pages
  251
- Publisher
  共立出版
- Data Source
  KAKENHI-PROJECT-20370061
[Journal Article] Mutual induced-fit mechanism drives binding between intrinsically disordered Bim and cryptic binding site of Bcl-xL2023
- Author(s)
  Bekker Gert-Jan、Araki Mitsugu、Oshima Kanji、Okuno Yasushi、Kamiya Narutoshi
- Journal Title
  
  Communications Biology
  
  Volume: 6 Issue: 1 Pages: 349-349
- DOI
  10.1038/s42003-023-04720-6
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20H03229
[Journal Article] Improvement of the Thermostability and Activity of the PET-Degrading Enzyme Cut190 toward a Detailed Understanding and Application of the Enzymatic Reaction Mechanism2023
- Author(s)
  Numoto Nobutaka, Kamiya Narutoshi, Oda Masayuki
- Journal Title
  
  ACS Books, Sustainable Green Chemistry in Polymer Research
  
  Volume: 1 Pages: 89-100
- DOI
  10.1021/bk-2023-1450.ch006
- ISBN
  9780841296930
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21H02120
[Journal Article] Advancing the field of computational drug design using multicanonical molecular dynamics-based dynamic docking2022
- Author(s)
  Bekker Gert-Jan、Kamiya Narutoshi
- Journal Title
  
  Biophysical Reviews
  
  Volume: 14 Issue: 6 Pages: 1349-1358
- DOI
  10.1007/s12551-022-01010-z
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-20H03229
[Journal Article] Thermal Stability Estimation of Single Domain Antibodies Using Molecular Dynamics Simulations2022
- Author(s)
  Bekker Gert-Jan、Kamiya Narutoshi
- Journal Title
  
  Methods in Molecular Biology
  
  Volume: 2552 Pages: 151-163
- DOI
  10.1007/978-1-0716-2609-2_8
- ISBN
  9781071626085, 9781071626092
- Data Source
  KAKENHI-PROJECT-20H03229
[Journal Article] Dynamic Docking Using Multicanonical Molecular Dynamics: Simulating Complex Formation at the Atomistic Level2021
- Author(s)
  Bekker Gert-Jan、Kamiya Narutoshi
- Journal Title
  
  Methods in Molecular Biology
  
  Volume: - Pages: 187-202
- DOI
  10.1007/978-1-0716-1209-5_11
- ISBN
  9781071612088, 9781071612095
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-20H03229
[Journal Article] Cutinases from thermophilic bacteria (actinomycetes): From identification to functional and structural characterization2021
- Author(s)
  Oda Masayuki、Numoto Nobutaka、Bekker Gert-Jan、Kamiya Narutoshi、Kawai Fusako
- Journal Title
  
  Methods in Enzymology
  
  Volume: - Pages: 159-185
- DOI
  10.1016/bs.mie.2020.12.031
- ISBN
  9780128220122
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-20H03229
[Journal Article] Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics2021
- Author(s)
  Araki Mitsugu、Matsumoto Shigeyuki、Bekker Gert-Jan、Isaka Yuta、Sagae Yukari、Kamiya Narutoshi、Okuno Yasushi
- Journal Title
  
  Nature Communications
  
  Volume: 12 Issue: 1 Pages: 1-10
- DOI
  10.1038/s41467-021-23157-1
- NAID
  120007041708
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-18K06594, KAKENHI-PROJECT-20H03229, KAKENHI-PROJECT-21K06510
[Journal Article] Cryptic-site binding mechanism of medium-sized Bcl-xL inhibiting compounds elucidated by McMD-based dynamic docking simulations2021
- Author(s)
  Bekker Gert-Jan、Fukuda Ikuo、Higo Junichi、Fukunishi Yoshifumi、Kamiya Narutoshi
- Journal Title
  
  Scientific Reports
  
  Volume: 11 Issue: 1 Pages: 5046-5046
- DOI
  10.1038/s41598-021-84488-z
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20H03229
[Journal Article] Accurate Binding Configuration Prediction of a G-Protein-Coupled Receptor to Its Antagonist Using Multicanonical Molecular Dynamics-Based Dynamic Docking2021
- Author(s)
  Bekker Gert-Jan、Araki Mitsugu、Oshima Kanji、Okuno Yasushi、Kamiya Narutoshi
- Journal Title
  
  Journal of Chemical Information and Modeling
  
  Volume: 61 Issue: 10 Pages: 5161-5171
- DOI
  10.1021/acs.jcim.1c00712
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-20H03229
[Journal Article] Dynamical Methods to Study Interaction in Proteins Facilitating Molecular Understanding of Cancer2021
- Author(s)
  Dasgupta Bhaskar、Bekker Gert-Jan、Kamiya Narutoshi
- Journal Title
  
  Handbook of Oxidative Stress in Cancer: Mechanistic Aspects
  
  Volume: - Pages: 1-17
- DOI
  10.1007/978-981-15-4501-6_149-1
- ISBN
  9789811545016
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-20H03229
[Journal Article] N-Terminal-Driven Binding Mechanism of an Antigen Peptide to Human Leukocyte Antigen-A*2402 Elucidated by Multicanonical Molecular Dynamic-Based Dynamic Docking and Path Sampling Simulations2021
- Author(s)
  Bekker Gert-Jan、Kamiya Narutoshi
- Journal Title
  
  The Journal of Physical Chemistry B
  
  Volume: 125 Issue: 49 Pages: 13376-13384
- DOI
  10.1021/acs.jpcb.1c07230
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-20H03229
[Journal Article] Difference of binding modes among three ligands to a receptor mSin3B corresponding to their inhibitory activities2021
- Author(s)
  Hayami Tomonori、Kamiya Narutoshi、Kasahara Kota、Kawabata Takeshi、Kurita Jun-ichi、Fukunishi Yoshifumi、Nishimura Yoshifumi、Nakamura Haruki、Higo Junichi
- Journal Title
  
  Scientific Reports
  
  Volume: 11 Issue: 1 Pages: 6178-6178
- DOI
  10.1038/s41598-021-85612-9
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20H03229
[Journal Article] Flexibility and cell permeability of cyclic Ras-inhibitor peptides revealed by coupled Nose Hoover equation2021
- Author(s)
  Kei Moritsugu, Koh Takeuchi, Narutoshi Kamiya, Junichi Higo, Isao Yasumatsu, Yoshifumi Fukunishi and Ikuo Fukuda
- Journal Title
  
  Journal of Chemical Information and Modeling
  
  Volume: 61 Issue: 4 Pages: 1921-1930
- DOI
  10.1021/acs.jcim.0c01427
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-20K03883, KAKENHI-PROJECT-20K11854, KAKENHI-PROJECT-20K21494, KAKENHI-PROJECT-17K05143, KAKENHI-PROJECT-18H02393, KAKENHI-PROJECT-20H03229
[Journal Article] Structural basis of mutants of <scp>PET</scp> ‐degrading enzyme from <i>Saccharomonospora viridis</i> <scp>AHK190</scp> with high activity and thermal stability2020
- Author(s)
  Emori Miho、Numoto Nobutaka、Senga Akane、Bekker Gert‐Jan、Kamiya Narutoshi、Kobayashi Yuma、Ito Nobutoshi、Kawai Fusako、Oda Masayuki
- Journal Title
  
  Proteins: Structure, Function, and Bioinformatics
  
  Volume: 89 Issue: 5 Pages: 502-511
- DOI
  10.1002/prot.26034
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-20H03229
[Journal Article] Molecular Interaction Mechanism of a 14-3-3 Protein with a Phosphorylated Peptide Elucidated by Enhanced Conformational Sampling2020
- Author(s)
  Higo Junichi、Kawabata Takeshi、Kusaka Ayumi、Kasahara Kota、Kamiya Narutoshi、Fukuda Ikuo、Mori Kentaro、Hata Yutaka、Fukunishi Yoshifumi、Nakamura Haruki
- Journal Title
  
  Journal of Chemical Information and Modeling
  
  Volume: 60 Issue: 10 Pages: 4867-4880
- DOI
  10.1021/acs.jcim.0c00551
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-20H03229
[Journal Article] Exhaustive search of the configurational space of heat‐shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking2020
- Author(s)
  Bekker Gert‐Jan、Araki Mitsugu、Oshima Kanji、Okuno Yasushi、Kamiya Narutoshi
- Journal Title
  
  Journal of Computational Chemistry
  
  Volume: 41 Issue: 17 Pages: 1606-1615
- DOI
  10.1002/jcc.26203
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-20H03229
[Journal Article] Coarse-Grained Diffraction Template Matching Model to Retrieve Multiconformational Models for Biomolecule Structures from Noisy Diffraction Patterns2020
- Author(s)
  Tokuhisa Atsushi、Kanada Ryo、Chiba Shuntaro、Terayama Kei、Isaka Yuta、Ma Biao、Kamiya Narutoshi、Okuno Yasushi
- Journal Title
  
  Journal of Chemical Information and Modeling
  
  Volume: 60 Issue: 6 Pages: 2803-2818
- DOI
  10.1021/acs.jcim.0c00131
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20H03229
[Journal Article] Dynamic Docking of a Medium-Sized Molecule to Its Receptor by Multicanonical MD Simulations2019
- Author(s)
  Bekker Gert-Jan、Araki Mitsugu、Oshima Kanji、Okuno Yasushi、Kamiya Narutoshi
- Journal Title
  
  The Journal of Physical Chemistry B
  
  Volume: 123 Issue: 11 Pages: 2479-2490
- DOI
  10.1021/acs.jpcb.8b12419
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16K07331
[Journal Article] Structural and thermodynamic characterization of endo-1,3-β-glucanase: Insights into the substrate recognition mechanism2018
- Author(s)
  M. Oda, S. Inaba, N. Kamiya, G.-J. Bekker, B. Mikami
- Journal Title
  
  Biochim. Biophys. Acta, Proteins Proteomics
  
  Volume: 1866 Issue: 3 Pages: 415-425
- DOI
  10.1016/j.bbapap.2017.12.004
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16K07331, KAKENHI-PROJECT-16H04909
[Journal Article] Folding thermodynamics of PET-hydrolyzing enzyme Cut190 depending on Ca2+ concentration2018
- Author(s)
  Inaba Satomi、Kamiya Narutoshi、Bekker Gert-Jan、Kawai Fusako、Oda Masayuki
- Journal Title
  
  Journal of Thermal Analysis and Calorimetry
  
  Volume: 135 Issue: 5 Pages: 2655-2663
- DOI
  10.1007/s10973-018-7447-9
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16K07331
[Journal Article] Thermal stability of single-domain antibodies estimated by molecular dynamics simulations2018
- Author(s)
  Bekker Gert-Jan、Ma Benson、Kamiya Narutoshi
- Journal Title
  
  Protein Science
  
  Volume: 28 Issue: 2 Pages: 429-438
- DOI
  10.1002/pro.3546
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16K07331
[Journal Article] Core Binding Site of a Thioflavin-T-Derived Imaging Probe on Amyloid β Fibrils Predicted by Computational Methods2018
- Author(s)
  Kawai Ryoko、Araki Mitsugu、Yoshimura Masashi、Kamiya Narutoshi、Ono Masahiro、Saji Hideo、Okuno Yasushi
- Journal Title
  
  ACS Chemical Neuroscience
  
  Volume: 9 Issue: 5 Pages: 957-966
- DOI
  10.1021/acschemneuro.7b00389
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16K07331
[Journal Article] Structural Dynamics of the PET-Degrading Cutinase-like Enzyme from Saccharomonospora viridis AHK190 in Substrate-Bound States Elucidates the Ca2+-Driven Catalytic Cycle2018
- Author(s)
  Numoto Nobutaka、Kamiya Narutoshi、Bekker Gert-Jan、Yamagami Yuri、Inaba Satomi、Ishii Kentaro、Uchiyama Susumu、Kawai Fusako、Ito Nobutoshi、Oda Masayuki
- Journal Title
  
  Biochemistry
  
  Volume: 57 Issue: 36 Pages: 5289-5300
- DOI
  10.1021/acs.biochem.8b00624
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16K07331
[Journal Article] Accurate prediction of complex structure and affinity for a flexible protein receptor and its inhibitor2017
- Author(s)
  G.-J. Bekker, N. Kamiya, M. Araki, I. Fukuda, Y. Okuno, H. Nakamura
- Journal Title
  
  J. Chem. Theory Comput.
  
  Volume: 13 Issue: 6 Pages: 2389-2399
- DOI
  10.1021/acs.jctc.6b01127
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16K07331, KAKENHI-PROJECT-16K14711
[Journal Article] Model building of antibody-antigen complex structures using GBSA scores2016
- Author(s)
  N. Shimba, N. Kamiya, H. Nakamura
- Journal Title
  
  J. Chem. Inf. Model.
  
  Volume: 56 Issue: 10 Pages: 2005-2012
- DOI
  10.1021/acs.jcim.6b00066
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-16K07331
[Journal Article] Elastic properties of dynein motor domain obtained from all-atom molecular dynamics simulations2016
- Author(s)
  Narutoshi Kamiya, Tadaaki Mashimo, Yu Takano, Takahide Kon, Genji Kurisu, Haruki Nakamura
- Journal Title
  
  Protein Engineering, Design and Selection
  
  Volume: 29 Issue: 8 Pages: 317-325
- DOI
  10.1093/protein/gzw022
- Peer Reviewed / Acknowledgement Compliant / Open Access
- Data Source
  KAKENHI-ORGANIZER-24118001, KAKENHI-PLANNED-24118008, KAKENHI-PROJECT-26291014, KAKENHI-PROJECT-26291034, KAKENHI-PROJECT-16K07331
[Journal Article] Revisiting Antibody Modeling Assessment for CDR-H3 loop2016
- Author(s)
  Hiroshi Nishigami, Narutoshi Kamiya, Haruki Nakamura
- Journal Title
  
  Protein Engineering, Design and Selection
  
  Volume: 29 Issue: 11 Pages: 477-484
- DOI
  10.1093/protein/gzw028
- Peer Reviewed / Acknowledgement Compliant / Open Access
- Data Source
  KAKENHI-ORGANIZER-24118001, KAKENHI-PLANNED-24118008, KAKENHI-PROJECT-16K07331, KAKENHI-PROJECT-16K14711
[Journal Article] The effect of conformational flexibility on binding free energy estimation between kinases and their inhibitors2016
- Author(s)
  M. Araki, N. Kamiya, M. Sato, M. Nakatsui, T. Hirokawa, Y. Okuno
- Journal Title
  
  J. Chem. Inf. Model.
  
  Volume: 56 Issue: 12 Pages: 2445-2456
- DOI
  10.1021/acs.jcim.6b00398
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-16K07331
[Journal Article] Specific non-local interactions are not necessary for recovering native protein dynamics2014
- Author(s)
  Dasgupta B, Kasahara K, Kamiya N, Nakamura H, Kinjo AR
- Journal Title
  
  PLoS ONE
  
  Volume: 9 Issue: 3 Pages: e91347-e91347
- DOI
  10.1371/journal.pone.0091347
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23370071, KAKENHI-PROJECT-25440070
[Journal Article] The Zero-multipole summation method for estimating electrostatic interactions in molecular dynamics : analysis of the accuracy and application to liquid systems2014
- Author(s)
  Fukuda I, Kamiya N, Nakamura H
- Journal Title
  
  J. Chem. Phys
  
  Volume: 140 Issue: 19 Pages: 194307-194307
- DOI
  10.1063/1.4875693
- NAID
  120005596268
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-23370071, KAKENHI-ORGANIZER-24118001, KAKENHI-PLANNED-24118008, KAKENHI-PROJECT-25390156, KAKENHI-PROJECT-25440070
[Journal Article] NMR Characterization of the Interaction of the Endonuclease Domain of MutL with Divalent Metal Ions and ATP2014
- Author(s)
  Mizushima R, Kim JK, Suetake I, Tanaka H, Takai T, Kamiya N, Takano Y, Mishima Y, Tajima S, Goto Y, Fukui K, *Lee YH
- Journal Title
  
  PLoS One
  
  Volume: 9 Issue: 6 Pages: e98554-e98554
- DOI
  10.1371/journal.pone.0098554
- NAID
  120006557621
- Peer Reviewed / Acknowledgement Compliant / Open Access
- Data Source
  KAKENHI-PROJECT-24570153, KAKENHI-PROJECT-25440070, KAKENHI-PROJECT-25870407
[Journal Article] Structure of the entire stalk region of the dynein motor domain2014
- Author(s)
  Yosuke Nishikawa, Takuji Oyama, Narutoshi Kamiya, Takahide Kon, Yoko Y. Toyoshima, Haruki Nakamura, Genji Kurisu
- Journal Title
  
  Journal of Molecular Biology
  
  Volume: 426 Issue: 19 Pages: 3232-3245
- DOI
  10.1016/j.jmb.2014.06.023
- Peer Reviewed
- Data Source
  KAKENHI-ORGANIZER-24118001, KAKENHI-PLANNED-24118008, KAKENHI-PROJECT-24370046, KAKENHI-PUBLICLY-25113504, KAKENHI-PUBLICLY-25117503, KAKENHI-PROJECT-25280109, KAKENHI-PROJECT-25291031, KAKENHI-PROJECT-25440070, KAKENHI-PROJECT-26291014, KAKENHI-PROJECT-26291034, KAKENHI-PROJECT-26440023
[Journal Article] Exhaustive comparison and classification of ligand-binding surfaces in proteins2013
- Author(s)
  Murakami Y, Kinoshita K, Kinjo AR, Nakamura H
- Journal Title
  
  Protein Science
  
  Volume: 22 Issue: 10 Pages: 1379-1391
- DOI
  10.1002/pro.2329
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-23370071, KAKENHI-ORGANIZER-24118001, KAKENHI-PLANNED-24118008
[Journal Article] Molecular dynamics simulations of a double-stranded DNA in an explicit solvent model with zero-dipole summation method2013
- Author(s)
  Arakawa T, Kamiya N, Nakamura H, Fukuda I
- Journal Title
  
  PLoS ONE
  
  Volume: 8 Issue: 10 Pages: e76606-e76606
- DOI
  10.1371/journal.pone.0076606
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-23370071, KAKENHI-ORGANIZER-24118001, KAKENHI-PLANNED-24118008, KAKENHI-PROJECT-25390156, KAKENHI-PROJECT-25440070
[Journal Article] Molecular Dynamics Simulations Accelerated by GPU for Biological Macromolecules with a Non-Ewald Scheme for Electrostatic Interactions2013
- Author(s)
  Mashimo T, Fukunishi Y, Kamiya N, Takano Y, Fukuda I, Nakamura H
- Journal Title
  
  J. Chem. Theory Comput
  
  Volume: 9 Issue: 12 Pages: 5599-5609
- DOI
  10.1021/ct400342e
- NAID
  120005604144
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23370071, KAKENHI-PROJECT-23657103, KAKENHI-PUBLICLY-25104717, KAKENHI-PROJECT-25390156, KAKENHI-PROJECT-25440070
[Journal Article]2013
- Author(s)
  N. Kamiya, I. Fukuda, H. Nakamura
- Journal Title
  
  Chem. Phys. Lett.
  
  Volume: 568-569 Pages: 26-32
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22570160
[Journal Article] Application of zero-dipole summation method to molecular dynamics2013
- Author(s)
  Narutoshi Kamiya
- Journal Title
  
  Chem. Phys. Lett.
  
  Volume: 568-569 Pages: 26-32
- DOI
  10.1016/j.cplett.2013.03.014
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22570160, KAKENHI-PROJECT-23370071, KAKENHI-PROJECT-23657103, KAKENHI-PLANNED-24118008, KAKENHI-PROJECT-25390156, KAKENHI-ORGANIZER-24118001
[Journal Article] Enhanced and effective conformational sampling of protein molecular systems for their free energy landscapes2012
- Author(s)
  Higo, J., Ikebe, J., Kamiya, N., Nakamura, H
- Journal Title
  
  Biophysical Rev
  
  Volume: 4 Issue: 1 Pages: 27-44
- DOI
  10.1007/s12551-011-0063-6
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-21113006, KAKENHI-PROJECT-22570160, KAKENHI-PROJECT-23370071
[Journal Article]2012
- Author(s)
  J. Higo, J. Ikebe, N. Kamiya, H. Nakamura
- Journal Title
  
  Biophys. Rev
  
  Volume: 4 Pages: 27-44
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22570160
[Journal Article]2012
- Author(s)
  I. Fukuda, N. Kamiya, Y. Yonezawa, H. Nakamura
- Journal Title
  
  J. Chem. Phys
  
  Volume: 137 Pages: 54314-54314
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22570160
[Journal Article] Simple and Accurate Scheme to Compute Electrostatic Interactions: Zero-dipole Summation Technique for Molecular System and Application to Bulk Water.2012
- Author(s)
  Ikuo Fukuda, Narutoshi Kamiya, Yasushige Yonezawa, Haruki Nakamura
- Journal Title
  
  Journal of Chemical Physics
  
  Volume: 137 Issue: 5 Pages: 54314-54314
- DOI
  10.1063/1.4739789
- NAID
  120005647641
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23370071, KAKENHI-PLANNED-24118008, KAKENHI-ORGANIZER-24118001
[Journal Article] Theory for trivial trajectory parallelization of multicanonical molecular dynamics and application to a polypeptide in water.2011
- Author(s)
  J.Ikebe, K.Umezawa, N.Kamiya, T.Sugihara, Y.Yonezawa, Y.Takano, H.Nakamura, J.Higo
- Journal Title
  
  J.Comput.Chem. 32
  
  Pages: 1286-1297
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-20370061
[Journal Article] Protein-inhibitor flexible docking by a multicanonical sampling: Native complex structure with the lowest free energy and a free-energy barrier distrinsuishing the native complex from the others.2007
- Author(s)
  N., Kamiya
- Journal Title
  
  BIOPHYSICS 3
  
  Pages: 75-84
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-18054013
[Presentation] PET分解酵素Cut190の高機能化と構造機能相関解析2024
- Author(s)
  近藤史弥、Gert-Jan Bekker、神谷成敏、沼本修孝、織田昌幸
- Organizer
  日本農芸化学会関西支部第529回講演会
- Data Source
  KAKENHI-PROJECT-21H02120
[Presentation] PET分解酵素Cut190のCa2+結合部位に着目した構造機能相関解析2023
- Author(s)
  近藤史弥、Gert-Jan Bekker、神谷成敏、沼本修孝、織田昌幸
- Organizer
  第96回日本生化学会大会
- Data Source
  KAKENHI-PROJECT-21H02120
[Presentation] PET分解酵素Cut190のアロステリック反応機構に基づく機能向上変異体の合理的設計2023
- Author(s)
  沼本修孝、Gert-Jan Bekker、神谷成敏、織田昌幸、伊藤暢聡
- Organizer
  第23回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-21H02120
[Presentation] 癌ワクチンペプチドと免疫関連タンパク質の結合自由エネルギー計算による親和性予測2021
- Author(s)
  神谷　成敏
- Organizer
  第8回HPCI成果報告会
- Data Source
  KAKENHI-PROJECT-20H03229
[Presentation] 癌ワクチンの個別医療化に向けたMHC受容体と癌ワクチンペプチドの結合自由エネルギー計算による親和性予測2020
- Author(s)
  神谷　成敏
- Organizer
  第７回HPCI成果報告会
- Data Source
  KAKENHI-PROJECT-20H03229
[Presentation] Thermal stability of single domain antibodies estimated by MD simulations2019
- Author(s)
  N. Kamiya, B. Ma, G.-J. Bekker
- Organizer
  The 63rd annual meeting of Biophysical Society, Baltimore Convention Center
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16K07331
[Presentation] クチナーゼの分子動力学計算による反応機構解析2019
- Author(s)
  神谷　成敏
- Organizer
  日本農芸化学会2019年度東京大会
- Invited
- Data Source
  KAKENHI-PROJECT-16K07331
[Presentation] Stability of single domain antibodies by molecular dynamics simulation2018
- Author(s)
  N. Kamiya, B. Ma, G.-J. Bekker
- Organizer
  The 32nd annual symposium of the Protein Society
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16K07331
[Presentation] マルチカノニカル分子動力学法によるタンパク質・リガンドのフレキシブルドッキング2018
- Author(s)
  神谷　成敏
- Organizer
  近畿化学協会コンピュータ化学部会公開講演会第１０１回例会
- Invited
- Data Source
  KAKENHI-PROJECT-16K07331
[Presentation] Binding mechanism of laminarihexaose to endo-1,3-βglucanase analyzed using molecular dynamics simulations2018
- Author(s)
  N. Kamiya, G.-J. Bekker, S. Inaba, B. Mikami, M. Oda
- Organizer
  The 62nd annual meeting of Biophysical Society
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16K07331
[Presentation] Estimation of single domain antibody stability by MD simulations2018
- Author(s)
  G.-J. Bekker, B. Ma, N. Kamiya
- Organizer
  第５６回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-16K07331
[Presentation] The effect of conformational flexibility on binding free energy estimation between protein kinases and their inhibitors2017
- Author(s)
  M. Araki, N. Kamiya, M. Sato, M. Nakatsui, T. Hirokawa, Y. Okuno
- Organizer
  The 61st annual meeting of Biophysical Society
- Place of Presentation
  ニューオリンズコンベンションセンター、ニューオリンズ（アメリカ）
- Year and Date
  2017-02-14
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16K07331
[Presentation] Multiscale simulations of cytoplasmic dynein: From all-atom to continuum mechanics2017
- Author(s)
  S. Iida, B. Hanson, N. Kamiya, G. Kurisu, T. Kon, H. Nakamura, S. Harris
- Organizer
  第５５回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-16K07331
[Presentation] Flexible docking between cyclin-dependent kinase 2 and its inhibitor CS3 using multicanonical MD and thermodynamic integration simulations2017
- Author(s)
  G.-J. Bekker, N. Kamiya, M. Araki, I. Fukuda, Y. Okuno, H. Nakamura
- Organizer
  第１７回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-16K07331
[Presentation] Prediction of complex structure and affinity between cyclin-dependent kinase 2 and its inhibitor using multicanonical molecular dynamics and thermodynamic integration simulations2017
- Author(s)
  N. Kamiya, G.-J. Bekker, M. Araki, I. Fukuda, Y. Okuno, H. Nakamura
- Organizer
  The 61st annual meeting of Biophysical Society
- Place of Presentation
  ニューオリンズコンベンションセンター、ニューオリンズ（アメリカ）
- Year and Date
  2017-02-15
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16K07331
[Presentation] Flexible docking and affinity calculation between CDK2 and its inhibitor CS3 using multicanonical MD and thermodynamic integration2017
- Author(s)
  G.-J. Bekker, N. Kamiya, M. Araki, I. Fukuda, Y. Okuno, H. Nakamura
- Organizer
  第５５回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-16K07331
[Presentation] Prediction of complex structure and affinity of CDK2 and its inhibitor using McMD and TI simulations2017
- Author(s)
  G.-J. Bekker, N. Kamiya, M. Araki, I. Fukuda, Y. Okuno, H. Nakamura
- Organizer
  The 19th IUBAM and the 11th EBSA congress
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16K07331
[Presentation] Flexible docking between cyclin-dependent kinase 2 and its inhibitor using multicanonical MD2016
- Author(s)
  G.-J.Bekker, N. Kamiya, M. Araki, Y. Okuno, H. Nakamura
- Organizer
  第５４回日本生物物理学会年会
- Place of Presentation
  つくば国際会議場、茨城県つくば市
- Year and Date
  2016-11-25
- Data Source
  KAKENHI-PROJECT-16K07331
[Presentation] An efficient new methodology for path elucidation and binding free energy calculation2016
- Author(s)
  Gert-Jan Bekker, Narutoshi Kamiya, Haruki Nakamura
- Organizer
  第16回日本蛋白質科学会年会
- Place of Presentation
  福岡国際会議場（福岡県、福岡市）
- Year and Date
  2016-06-07
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] Ligand binding studies of the nuclear receptor PPARgamma using FRET and MD2016
- Author(s)
  N. Kamiya, T. Shiraki
- Organizer
  The 60th annual meeting of Biophysical Society
- Place of Presentation
  Los Angeles convention center, Los Angeles, USA
- Year and Date
  2016-02-28
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25440070
[Presentation] 分子シミュレーションにおける静電相互作用計算法：零多重極子法の理論と実際2016
- Author(s)
  福田育夫, Wang Han, 神谷成敏, 笠原浩太, 寺田透, 櫻庭俊, 中村春木
- Organizer
  第54回日本生物物理学会年会
- Place of Presentation
  つくば国際会議場（茨城県、つくば市）
- Year and Date
  2016-11-25
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] The effect of conformational flexibility on the binding free energy calculation between kinases and their ATP-conpetitive inhibitors2016
- Author(s)
  M. Araki, N. Kamiya, M. Sato, M. Nakatsui, T. Hirokawa, Y. Okuno
- Organizer
  第５４回日本生物物理学会年会
- Place of Presentation
  つくば国際会議場、茨城県つくば市
- Year and Date
  2016-11-26
- Data Source
  KAKENHI-PROJECT-16K07331
[Presentation] 巨大生体分子の長時間 MD シミュレーションの開発と生体分子の構造機能相関の解明2016
- Author(s)
  鷹野優、Neetha Mohan、草鹿あゆみ、川端猛、笠原浩太、真下忠彰、神谷成敏、中村春木
- Organizer
  第８回「学際計算科学による新たな知の発展・統合・創出」シンポジウム
- Place of Presentation
  筑波大学計算科学研究センター（茨城県、つくば市）
- Year and Date
  2016-10-17
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] Computational method for electrostatic interactions in molecular simulation: theory and practice in the zero-multipole summation2016
- Author(s)
  I. Fukuda, H. Wang, N. Kamiya, K. Kasahara, T. Terada, S. Sakuraba, H. Nakamura
- Organizer
  第５４回日本生物物理学会年会
- Place of Presentation
  つくば国際会議場、茨城県つくば市
- Year and Date
  2016-11-26
- Data Source
  KAKENHI-PROJECT-16K07331
[Presentation] Multiscale simulation of cytoplasmic dynein: From all-atom to continuum mechanics2016
- Author(s)
  S. Iida, B. Hanson, N. Kamiya, G. Kurisu, T. Kon, H. Nakamura, S. Harris
- Organizer
  第５４回日本生物物理学会年会
- Place of Presentation
  つくば国際会議場、茨城県つくば市
- Year and Date
  2016-11-25
- Data Source
  KAKENHI-PROJECT-16K07331
[Presentation] Flexible docking between cyclin-dependent kinase 2 and its inhibitor using multicanonical MD2016
- Author(s)
  Gert-Jan Bekker, Narutoshi Kamiya, Mitsugu Araki, Yasushi Okuno, Haruki Nakamura
- Organizer
  第54回日本生物物理学会年会
- Place of Presentation
  つくば国際会議場（茨城県、つくば市）
- Year and Date
  2016-11-25
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] A novel method to determine the optimal unbinding path between receptor and ligand using advanced molecular dynamics simulation2015
- Author(s)
  Gert-Jan Bekker, 神谷成敏, 中村春木
- Organizer
  第53回日本生物物理学会年会
- Place of Presentation
  金沢大学角間キャンパス（金沢市）
- Year and Date
  2015-09-13
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] Accurate ensemble modeling of CDR-H3 loop in antibody2015
- Author(s)
  H. Nishigami, G.-J. Bekker, N. Kamiya, J. Higo, H. Nakamura
- Organizer
  第５３回日本生物物理学会年会
- Place of Presentation
  金沢大学　角間キャンパス, 金沢
- Year and Date
  2015-09-13
- Data Source
  KAKENHI-PROJECT-25440070
[Presentation] FRET法とRAMD法を用いた核内受容体PPARγのリガンド結合に関する実験・理論的研究2015
- Author(s)
  神谷成敏, Gert-Jan Bekker, 白木琢磨, 中村春木
- Organizer
  第15回日本蛋白質科学会年会
- Place of Presentation
  あわぎんホール（徳島市）
- Year and Date
  2015-06-24
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] FRET法とRAMD法を用いた核内受容体PPARγのリガンド結合に関する実験・理論的研究2015
- Author(s)
  神谷　成敏、ベッカー　ガージャン、白木　琢磨、中村　春木
- Organizer
  第１５回日本蛋白質科学会年会
- Place of Presentation
  あわぎんホール, 徳島
- Year and Date
  2015-06-24
- Data Source
  KAKENHI-PROJECT-25440070
[Presentation] Development and application of novel non-Ewald methods for calculating electrostatic interactions in molecular simulations2015
- Author(s)
  I. Fukuda, N. Kamiya, H. Wang, K. Kasahara, H. Nakamura
- Organizer
  The 29th annual symposium of the Protein Society
- Place of Presentation
  Fira de Barcelona, Barcelona, Spain
- Year and Date
  2015-07-23
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25440070
[Presentation] A novel method to determine the optimal unbinding path between receptor and ligand using advanced molecular dynamics simulations2015
- Author(s)
  G.-J. Bekker, N. Kamiya, H. Nakamura
- Organizer
  第５３回日本生物物理学会年会
- Place of Presentation
  金沢大学　角間キャンパス, 金沢
- Year and Date
  2015-09-13
- Data Source
  KAKENHI-PROJECT-25440070
[Presentation] 分子シミュレーションにおける静電相互作用計算のための新規非エバルト法2015
- Author(s)
  福田育夫, 神谷成敏, Han Wang, 笠原浩太、中村春木
- Organizer
  第53回日本生物物理学会年会
- Place of Presentation
  金沢大学角間キャンパス（金沢市）
- Year and Date
  2015-09-13
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] In-vitro and in-silico studies of ligand binding to the nuclear receptor PPARgamma using FRET and MD2015
- Author(s)
  N. Kamiya, G.-J. Bekker, T. Shiraki, H. Nakamura
- Organizer
  The 29th annual symposium of the Protein Society
- Place of Presentation
  Fira de Barcelona, Barcelona, Spain
- Year and Date
  2015-07-23
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25440070
[Presentation] 抗体CDR-H3ループ領域の立体構造予測2015
- Author(s)
  西上博士, Gert-Jan Bekker, 神谷成敏, 肥後順一, 中村春木
- Organizer
  第53回日本生物物理学会年会
- Place of Presentation
  金沢大学角間キャンパス（金沢市）
- Year and Date
  2015-09-13
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] p53蛋白質C末端天然変性領域の構造探索2015
- Author(s)
  飯田慎仁, 神谷成敏, 北條裕信, 中村春木, 肥後順一
- Organizer
  第15回日本蛋白質科学会年会
- Place of Presentation
  あわぎんホール（徳島市）
- Year and Date
  2015-06-24
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] Molecular dynamics simulations of dynein motor domain in explicit water2014
- Author(s)
  N. Kamiya, T. Mashimo, Y. Takano, T. Kon, G. Kurisu, H. Nakamura
- Organizer
  Biophysical society 58th annual meeting
- Place of Presentation
  Moscone center, San Francisco, USA
- Data Source
  KAKENHI-PROJECT-25440070
[Presentation] Contact number diffusion model for the normal mode analysis of protein structure2014
- Author(s)
  Bhaskar Dasgupta, Kota Kasahara, Narutoshi Kamiya, Haruki Nakamura, Akira Kinjo
- Organizer
  第52回日本生物物理学会年会
- Place of Presentation
  札幌コンベンションセンター
- Year and Date
  2014-09-26
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] Elastic properties of dynein motor domain obatined from all-atom molecular dynamics simulations in explicit water2014
- Author(s)
  Narutoshi Kamiya, Tadaaki Mashimo, Yu Takano, Takahide Kon, Genji Kurisu, Haruki Nakamura
- Organizer
  第52回日本生物物理学会年会
- Place of Presentation
  札幌コンベンションセンター
- Year and Date
  2014-09-25
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] A comparison of 3D conformations of endothelin-1 analogs to find the pharmacophore model required for endothelin ligand2014
- Author(s)
  B. Ma, T. Kawabata, N. Kamiya, H. Nakamura
- Organizer
  Biophysical society 58th annual meeting
- Place of Presentation
  Moscone center, San Francisco, USA
- Data Source
  KAKENHI-PROJECT-25440070
[Presentation] All-atom molecular dynamics simulations of dynein motor domain in explicit water2013
- Author(s)
  Narutoshi Kamiya, Tadaaki Mashimo, Yu Takano, Takahide Kon, Genji Kurisu, Haruki Nakamura
- Organizer
  Protein Society the 27th Annual Symposium
- Place of Presentation
  Boston（USA）
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] All-atom molecular dynamics simulations of dynein motor domain in explicit water2013
- Author(s)
  Narutoshi Kamiya, Tadaaki Mashimo, Yu Takano, Takahide Kon, Genji Kurisu, Haruki Nakamura
- Organizer
  Protein Society the 27th Annual Symposium
- Place of Presentation
  Boston Marriott, Boston, USA
- Data Source
  KAKENHI-PROJECT-23370071
[Presentation] Crystal structure of endo-1,3-beta-glucanase and its binding to laminarioligosaccharide2013
- Author(s)
  M. Oda, Y. Tanabe, N. Komichi, N. Kamiya, H. Nakamura, B. Mikami
- Organizer
  The 27th annual symposium of the protein society
- Place of Presentation
  Boston marriott copley place, Boston, USA
- Data Source
  KAKENHI-PROJECT-25440070
[Presentation] Zero-dipole summation method for evaluating eletrostatic interaction in molecular simulation of biomolecular system2013
- Author(s)
  Ikuo Fukuda, Narutoshi Kamiya, Haruki Nakamura
- Organizer
  第51回日本生物物理学会年会
- Place of Presentation
  国立京都国際会館（京都市）
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] All-atom molecular dynamics simulations of dynein motor domain in explicit water2013
- Author(s)
  N. Kamiya, T. Mashimo, Y. Takano, T. Kon, G. Kurisu, H. Nakamura
- Organizer
  Dynein 2013 international workshop
- Place of Presentation
  Orbis Hall, Kobe, Japan
- Data Source
  KAKENHI-PROJECT-25440070
[Presentation] The zero-dipole summation method and its application to molecular simulation with homogenous and inhomogeneous systems2013
- Author(s)
  Ikuo Fukuda, Narutoshi Kamiya, Kota Kasahara, Haruki Nakamura
- Organizer
  The 12th Asia Pacific Physics Conference (APPC12)
- Place of Presentation
  幕張メッセ（千葉市）
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] All-atom molecular dynamics simulations of dynein motor domain in explicit water2013
- Author(s)
  N. Kamiya, T. Mashimo, Y. Takano, T. Kon, G. Kurisu, H. Nakamura
- Organizer
  The 27th annual symposium of the protein society
- Place of Presentation
  Boston marriott copley place, Boston, USA
- Data Source
  KAKENHI-PROJECT-25440070
[Presentation] All-atomic molecular dynamics simulations of dynein motor domain in explicit water2013
- Author(s)
  Narutoshi Kamiya, Tadaaki Mashimo, Yu Takano, Takahide Kon, Genji Kurisu, Haruki Nakamura
- Organizer
  第13回日本蛋白質科学会年会
- Place of Presentation
  とりぎん文化会館（鳥取市）
- Data Source
  KAKENHI-PROJECT-23370071
[Presentation] Zero-dipole summation method for evaluating eletrostatic interaction in molecular simulation of biomolecular system2013
- Author(s)
  Ikuo Fukuda, Narutoshi Kamiya, Haruki Nakamura
- Organizer
  第51回日本生物物理学会年会
- Place of Presentation
  国立京都国際会館
- Data Source
  KAKENHI-PROJECT-23370071
[Presentation] Molecular dynamics simulation of dynein motor domain in explicit water2012
- Author(s)
  Narutoshi Kamiya
- Organizer
  日本生物物理学会
- Place of Presentation
  名古屋大学
- Data Source
  KAKENHI-PROJECT-22570160
[Presentation] Molecular dynamics simulations of dynein motor domain in explicit water2012
- Author(s)
  N. Kamiya, T. Mashimo, Y. Takano, T. Kon, G. Kurisu, H. Nakamura
- Organizer
  日本生物物理学会年会
- Place of Presentation
  愛知県名古屋市
- Year and Date
  2012-09-24
- Data Source
  KAKENHI-PROJECT-22570160
[Presentation] Molecular dynamics simulations of dynein motor domain in explicit water2012
- Author(s)
  神谷　成敏
- Organizer
  第50回日本生物物理学会年会
- Place of Presentation
  名古屋大学東山キャンパス
- Data Source
  KAKENHI-PROJECT-23370071
[Presentation] Molecular Dynamics Simulations of Ets1-DNA complexes using Zero-Dipole Summation Method2012
- Author(s)
  Takamasa Arakawa, Masaaki Shiina, Kazuhiro Ogata, Narutoshi Kamiya, Ikuo Fukuda, Haruki Nakamura
- Organizer
  第50回日本生物物理学会年会
- Place of Presentation
  名古屋大学
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] A simple non-Ewald scheme: the zero-dipole summation method and its application to molecular systems2012
- Author(s)
  Ikuo Fukuda, Narutoshi Kamiya, Takamasa Arakawa, Haruki Nakamura
- Organizer
  Conference on Computational Physics (CCP2012)
- Place of Presentation
  ニチイ学館・神戸ポートアイランドセンター
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] Flexible docking between antigen and antibody by multicanonical molecular dynamics simulation2012
- Author(s)
  N. Kamiya, J. Higo, H. Nakamura
- Organizer
  日本生物物理学会年会
- Place of Presentation
  兵庫県姫路市
- Year and Date
  2012-09-18
- Data Source
  KAKENHI-PROJECT-22570160
[Presentation] 抗原-抗体間のフレキシブルドッキング・マルチカノニカル分子動力学シミュレーション2011
- Author(s)
  神谷成敏、肥後順一、中村春木
- Organizer
  日本蛋白質科学会年会
- Place of Presentation
  大阪府吹田市
- Year and Date
  2011-06-09
- Data Source
  KAKENHI-PROJECT-22570160
[Presentation] 抗原・抗体間のフレキシブルドッキング・マルチカノニカル分子動力学シミュレーション2011
- Author(s)
  神谷　成敏
- Organizer
  第11回日本蛋白質科学会年会
- Place of Presentation
  大阪千里
- Data Source
  KAKENHI-PROJECT-23370071
[Presentation] Flexible docking between antigen and antibody by multicanonical molecular dynamics simulation2011
- Author(s)
  N.Kamiya, J.Higo, H.Nakamura
- Organizer
  日本生物物理学会学会
- Place of Presentation
  兵庫県姫路市
- Year and Date
  2011-09-18
- Data Source
  KAKENHI-PROJECT-22570160
[Presentation] 抗原-抗体間のフレキシブルドッキング・マルチカノニカル分子動力学シミュレーション2011
- Author(s)
  神谷成敏、肥後順一、中村春木
- Organizer
  日本蛋白質科学会
- Place of Presentation
  大阪府吹田市
- Year and Date
  2011-06-09
- Data Source
  KAKENHI-PROJECT-22570160
[Presentation] Conformational transitions in the CDRH3 region of the antidansyl monoclonal antibody by molecular dynamics simulations2010
- Author(s)
  N. Kamiya, J. Ikebe, K. Umezawa, Y. Yonezawa, J. Higo, H. Nakamura
- Organizer
  日本生物物理学会年会
- Place of Presentation
  宮城県仙台市
- Year and Date
  2010-09-20
- Data Source
  KAKENHI-PROJECT-22570160
[Presentation] Conformational transitions in the CDRH3 region of the anti-dansyl monoclonal antibody by molecular dynamics simulations2010
- Author(s)
  Narutoshi Kamiya, et al.
- Organizer
  第48回日本生物物理学会年会
- Place of Presentation
  東北大学・川内北キャンパス(宮城県仙台市)
- Year and Date
  2010-09-20
- Data Source
  KAKENHI-PROJECT-22570160
[Presentation] Structural transitions in the CDRH3 region of the anti-dansyl monoclonal antibody by molecular dynamics simulations2010
- Author(s)
  Narutoshi Kamiya, et al.
- Organizer
  CBI Sceiety 2010
- Place of Presentation
  学術総合センター(東京都千代田区)
- Year and Date
  2010-09-15
- Data Source
  KAKENHI-PROJECT-22570160
[Presentation] Model building of antibody-antigen complex structures using GB/SA scores
- Author(s)
  N. Kamiya, N. Shimba, H. Nakamura
- Organizer
  The 28th annual meeting of the protein society
- Place of Presentation
  The Manchester grand Hyatt San Diego, San Diego, USA
- Year and Date
  2014-07-27 – 2014-07-30
- Data Source
  KAKENHI-PROJECT-25440070
[Presentation] Zero-dipole summation method for evaluating eletrostatic interaction in molecular simulation of biomolecular system.
- Author(s)
  Ikuo Fukuda, Narutoshi Kamiya, Haruki Nakamura
- Organizer
  第51回日本生物物理学会年会
- Place of Presentation
  国立京都国際会館（京都市）
- Year and Date
  2013-10-28 – 2013-10-30
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] A simple non-Ewald scheme for calculating electrostatic interactions of charged particle systems: the zero-dipole summation method and the application to molecular systems
- Author(s)
  Ikuo Fukuda, Narutoshi Kamiya, Takamasa Arakawa, Tadaaki Mashimo, Yu Takano, Haruki Nakamura
- Organizer
  2013年ハイパフォーマンスコンピューティングと計算科学シンポジウム
- Place of Presentation
  東京工業大学蔵前会館
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] The zero-dipole summation method and its application to molecular simulation with homogenous and inhomogeneous systems
- Author(s)
  Ikuo Fukuda, Narutoshi Kamiya, Kota Kasahara, Haruki Nakamura
- Organizer
  The 12th Asia Pacific Physics Conference (APPC12)
- Place of Presentation
  幕張メッセ（千葉市）大手町サンスカイルーム（東京）
- Year and Date
  2013-07-15 – 2013-07-16
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] A simple non-Ewald scheme for calculating electrostatic interactions of charged particle systems: the zero-dipole summation method and the application to molecular systems
- Author(s)
  Ikuo Fukuda1, Narutoshi Kamiya, Takamasa Arakawa, Tadaaki Mashimo, Yu Takano, Haruki Nakamura
- Organizer
  2013年ハイパフォーマンスコンピューティングと計算科学シンポジウム
- Place of Presentation
  東京工業大学蔵前会館
- Data Source
  KAKENHI-PROJECT-23370071
[Presentation] Molecular dynamics study on evaluation of a decoy set generated by docking between antibody and antigen
- Author(s)
  N. Kamiya, N. Shimba, H. Nakamura
- Organizer
  The 4th Asia pacific protein association conference
- Place of Presentation
  International convention center, Jeju, Korea
- Year and Date
  2014-05-17 – 2014-05-20
- Data Source
  KAKENHI-PROJECT-25440070
[Presentation] All-atomic molecular dynamics simulations of dynein motor domain in explicit water
- Author(s)
  Narutoshi Kamiya, Tadaaki Mashimo, Yu Takano, Takahide Kon, Genji Kurisu, Haruki Nakamura
- Organizer
  第13回日本蛋白質科学会年会
- Place of Presentation
  とりぎん文化会館（鳥取市）
- Year and Date
  2013-06-12 – 2013-06-14
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] 溶媒を陽に考慮した全原子分子動力学シミュレーションから得られたダイニンの弾性
- Author(s)
  N. Kamiya, T. Mashimo, Y. Takano, T. Kon, G. Kurisu, H. Nakamura
- Organizer
  生物物理学会第５２回年会
- Place of Presentation
  札幌コンベンションセンター、札幌
- Year and Date
  2014-09-25 – 2014-09-27
- Data Source
  KAKENHI-PROJECT-25440070
[Presentation] GPU-accelerated calculation of electrostatic interactions with zero-dipole summation method
- Author(s)
  Tadaaki Mashimo, Yoshifumi Fukunishi, Ikuo Fukuda, Narutoshi Kamiya, Yu Takano, Haruki Nakamura
- Organizer
  2013年ハイパフォーマンスコンピューティングと計算科学シンポジウム
- Place of Presentation
  東京工業大学蔵前会館
- Data Source
  KAKENHI-PROJECT-23370071
[Presentation] 抗原抗体ドッキングのデコイセット評価法
- Author(s)
  榛葉　教子、神谷　成敏、中村　春木
- Organizer
  第１４回日本蛋白質科学会年会
- Place of Presentation
  ワークピア横浜、横浜
- Year and Date
  2014-06-25 – 2014-06-27
- Data Source
  KAKENHI-PROJECT-25440070
[Presentation] All-atom molecular dynamics simulations of dynein motor domain in explicit water
- Author(s)
  Narutoshi Kamiya, Tadaaki Mashimo, Yu Takano, Takahide Kon, Genji Kurisu, Haruki Nakamura
- Organizer
  Protein Society the 27th Annual Symposium
- Place of Presentation
  Boston Marriott, Copley Place, Boston, USA
- Year and Date
  2013-07-20 – 2013-07-23
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] GPU-accelerated calculation of electrostatic interactions with zero-dipole summation method
- Author(s)
  Tadaaki Mashimo, Yoshifumi Fukunishi, Ikuo Fukuda, Narutoshi Kamiya, Yu Takano, Haruki Nakamura
- Organizer
  2013年ハイパフォーマンスコンピューティングと計算科学シンポジウム
- Place of Presentation
  東京工業大学蔵前会館
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] Elastic property of dynein motor domain obtained from all-atom molecular dynamics simulations in explicit water
- Author(s)
  N. Kamiya, T. Mashimo, Y. Takano, T. Kon, G. Kurisu, H. Nakamura
- Organizer
  Biophysical society 59th annual meeting
- Place of Presentation
  Baltimore convention center, Baltimore, USA
- Year and Date
  2015-02-07 – 2015-02-11
- Data Source
  KAKENHI-PROJECT-25440070

1. NAKAMURA Haruki (80134485)

# of Collaborated Projects: 5 results

# of Collaborated Products: 38 results
2. YONEZAWA Yasushige (40248753)

# of Collaborated Projects: 3 results

# of Collaborated Products: 1 results
3. HIGO Junichi (80265719)

# of Collaborated Projects: 2 results

# of Collaborated Products: 3 results
4. Oda Masayuki (20318231)

# of Collaborated Projects: 2 results

# of Collaborated Products: 6 results
5. KINOSHITA Kengjo (60332293)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
6. KINJO Akira R (30370117)

# of Collaborated Projects: 1 results

# of Collaborated Products: 2 results
7. KONO Hidetoshi (40291918)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
8. KASAHARA Kota (90634965)

# of Collaborated Projects: 1 results

# of Collaborated Products: 6 results
9. 中島伸介 (60324852)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
10. 鷹野優 (30403017)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
11. 大島勘二 (40437330)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
12. 藤井聡 (40452825)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
13. 皿井明倫 (20221286)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
14. 伊藤暢聡 (40361703)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
15. Bekker Gerardu (80813758)

# of Collaborated Projects: 1 results

# of Collaborated Products: 11 results
16. 関口博史 (00401563)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
17. 沼本修孝 (20378582)

# of Collaborated Projects: 1 results

# of Collaborated Products: 4 results
18. 宮ノ入洋平 (80547521)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
19. IIDA Midori

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
20. ISHI Shunsuke

# of Collaborated Projects: 0 results

# of Collaborated Products: 2 results
21. 荒木望嗣

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
22. 末武勲

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
23. 森次圭

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

Kamiya Narutoshi 神谷 成敏

KAMIYA Narutoshi 神谷 成敏

神谷 成敏 カミヤ ナルトシ

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T細胞受容体に対するデータ駆動型分子デザイン法の開発Principal Investigator

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Structural dynamics of cutinase Cut190 upon Ca2+ binding and molecular mechanism of PET degradation by Cut190

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Complex structure and affinity prediction among cancer vaccine peptides and immune related proteinsPrincipal Investigator

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Accurate predictions of complex structure and affinity between proteins and drugsPrincipal Investigator

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Development of a complex structure prediction method between proteins using binding free-energy as a scoring functionPrincipal Investigator

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Elucidation of information-processing mechanisms during transcription cycle using computational and information sciences

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Quantitative computational and informatics studies on protein-protein interaction systems based on their dynamic structures

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Development of the free-energy evaluation method between protein and drug moleculesPrincipal Investigator

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Structural Interactome Studies from Computational and Bioinformatics Approaches

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分子シミュレーション支援による生体超分子複合体の構造機能相関の理論的研究

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分子シミュレーション支援による生体超分子複合体の構造・機能解析

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[Book] タンパク質計算科学2009

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[Journal Article] Mutual induced-fit mechanism drives binding between intrinsically disordered Bim and cryptic binding site of Bcl-xL2023

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Kamiya Narutoshi 神谷成敏

KAMIYA Narutoshi 神谷成敏

神谷成敏カミヤナルトシ