Takefumi Yamashita 山下雄史

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Yamashita Takefumi 山下雄史

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Researcher Number	50615622
Other IDs
Affiliation (Current)	2025: 星薬科大学, 薬学部, 准教授 2025: 東京大学, 先端科学技術研究センター, 特任准教授
Affiliation (based on the past Project Information) *help	2025: 星薬科大学, 薬学部, 准教授 2023: 星薬科大学, 薬学部, 准教授 2015 – 2023: 東京大学, 先端科学技術研究センター, 特任准教授
Review Section/Research Field	Principal Investigator Basic Section 32010:Fundamental physical chemistry-related / Basic Section 13040:Biophysics, chemical physics and soft matter physics-related / Mathematical Sciences in Search of New Cooperation Except Principal Investigator Basic Section 52040:Radiological sciences-related / Biomolecular chemistry / Transition State Control / Physical chemistry
Keywords	Principal Investigator シミュレーション / 分子ダイナミクス / タンパク質 / 分子動力学 / 分子動力学シミュレーション / 細胞状態 / 形態形成 / 細胞間相互作用 / 領域形成 / 細胞分化 … More / タンパク質-タンパク質相互作用 / 深層学習 / ２次元カオス系 / データベース / 古典力学 / 抗体 / タンパク質間相互作用 / 機械学習 / 解析理論 / タンパク質-リガンド相互作用 / 構造解析 / 計算幾何 / エントロピー / 分子設計 / 生体分子 / ダイナミクス変化 / 分子シミュレーション / 時系列解析 / 計算幾何学 / 数理科学 / 分子生物学 … More Except Principal Investigator ドジメトリー / アスタチン-211 / アビジン / ビオチン / α線 / アイソトープ治療 / アスタチン / プレターゲティング / コンピュータシミュレーション / 分子認識 / スプライシング / タンパク質相互作用 / ヒストン / 血管内皮細胞 / オルタナティブスプライシング / パターン認識受容体 / 自然免疫 / 細胞周期 / RNAプロセッシング / ペントラキシン / ヒストン障害 / 敗血症 / 反応境界 / 化学反応動力学 / クラスター / 溶媒効果 / 化学物理 / 異性化反応 / 相空間構造 / 反応性境界 / エネルギー移動 / 機械学習 / 反応動力学 / 電子状態揺らぎ / 電荷分離 / 励起状態化学反応 / 超高縮重励起状態化学 / 超高速化学反応動力学 / 非断熱電子動力学 / 化学動力学 / 励起状態化学 / 非断熱動力学 / 超高速化学反応 / 縮重状態 / レーザー化学 / 励起状態動力学超高速化学反応 / 励起状態動力学 / 非断熱遷移 / 電子ダイナミクス / 時間領域量子化学 / プロトン移動 / 電子移動 / 非断熱化学動力学 / 電子動力学 Less

高分子アモルファスのマルチスケールシミュレーション技術の基礎理論の確立と実践Principal Investigator
- Principal Investigator
  
  山下雄史
- Project Period (FY)
  2025 – 2028
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Review Section
  
  Basic Section 32010:Fundamental physical chemistry-related
- Research Institution
  Hoshi University
１細胞計測に基づく細胞モデルとそれに基づく形態形成の理論の開発Principal Investigator
- Principal Investigator
  
  山下雄史
- Project Period (FY)
  2021 – 2024
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Review Section
  
  Basic Section 13040:Biophysics, chemical physics and soft matter physics-related
- Research Institution
  Hoshi University
  The University of Tokyo
Optimization of pretargeted alpha therapy for multiple types of cancer
- Principal Investigator
  
  Washiyama Kohshin
- Project Period (FY)
  2020 – 2022
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 52040:Radiological sciences-related
- Research Institution
  Fukushima Medical University
Dynamics of protein-protein interface: Development of analysis methods based on machine learning and MD simulationPrincipal Investigator
- Principal Investigator
  
  Yamashita Takefumi
- Project Period (FY)
  2018 – 2022
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Review Section
  
  Basic Section 32010:Fundamental physical chemistry-related
- Research Institution
  The University of Tokyo
Theoretical elucidation of dynamical solvent effects in controling chemical reactions
- Principal Investigator
  
  Kawai Shinnosuke
- Project Period (FY)
  2016 – 2022
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Research Field
  
  Transition State Control
- Research Institution
  Shizuoka University
Development of Molecular Dynamics Classification Theories for Life Science and Drug DesignPrincipal Investigator
- Principal Investigator
  
  Yamashita Takefumi
- Project Period (FY)
  2015 – 2019
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Research Field
  
  Mathematical Sciences in Search of New Cooperation
- Research Institution
  The University of Tokyo
Nonadiabatic Electron Dynamics in Chemistry of Charge Separation, Proton Transfer, Electron Transmission, and Huge Electronic-State Fluctuation
- Principal Investigator
  
  Takatsuka Kazuo
- Project Period (FY)
  2015 – 2019
- Research Category
  
  Grant-in-Aid for Scientific Research (S)
- Research Field
  
  Physical chemistry
- Research Institution
  Kyoto University
  The University of Tokyo
Dynamics of Molecular Pattern Recognition in Protein Interaction
- Principal Investigator
  
  HAMAKUBO TAKAO
- Project Period (FY)
  2013 – 2017
- Research Category
  
  Grant-in-Aid for Scientific Research (S)
- Research Field
  
  Biomolecular chemistry
- Research Institution
  The University of Tokyo

All 2022 2021 2020 2019 2018 2017 2016 2015 2013 Other

All Journal Article Presentation Other

[Journal Article] Effect of N343 glycosylation and N501Y mutation on the SARS-CoV-2 spike protein: Modeling and MD Simulations2022
- Author(s)
  Yamashita Takefumi、Mitsui Takashi、Sasaki Kohei、Wada Mitsuhito、Matsuura Azuma、Kamiya Nozomu
- Journal Title
  
  AIP Conf. Proc.
  
  Volume: 2611 Pages: 020008-020008
- DOI
  10.1063/5.0119713
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-18K05025
[Journal Article] Singular spectrum transformation for detecting molecular motion mode change of protein systems2021
- Author(s)
  Yamashita Takefumi、Shoji Naoyuki
- Journal Title
  
  AIP Conf. Proc.
  
  Volume: 2343 Pages: 020010-020010
- DOI
  10.1063/5.0047736
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-18K05025
[Journal Article] 抗体医薬品設計に IT 革命を: 理論と計算による挑戦2019
- Author(s)
  山下雄史
- Journal Title
  
  月刊「細胞」(The Cell)
  
  Volume: 51 Pages: 344-347
- Data Source
  KAKENHI-PROJECT-15KT0103
[Journal Article] A SNP in a Steroidogenic Enzyme Is Associated with Phenotypic Sex in Seriola Fishes2019
- Author(s)
  T. Koyama, M. Nakamoto#, K. Morishima#, R. Yamashita#, T. Yamashita#, K. Sasaki, Y. Kuruma, N. Mizuno, M. Suzuki, K. Okada, R. Ieda, T. Uchino, S. Tasumi, S. Hosoya, S. Uno, J. Koyama, A. Toyoda, K. Kikuchi, T. Sakamoto
- Journal Title
  
  Current Biology
  
  Volume: 29 Issue: 11 Pages: 1901-1909
- DOI
  10.1016/j.cub.2019.04.069
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-15H05752, KAKENHI-PROJECT-15KT0103, KAKENHI-PROJECT-16H06279, KAKENHI-PROJECT-18H02277
[Journal Article] Convergence in LINE-1 nucleotide variations can benefit redundantly forming triplexes with lncRNA in mammalian X-chromosome inactivation2019
- Author(s)
  Y. Matsuno, T. Yamashita, M. Wagatsuma and H. Yamakage
- Journal Title
  
  Mobile DNA
  
  Volume: 10 Issue: 1 Pages: 33-33
- DOI
  10.1186/s13100-019-0173-4
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-15H05752
[Journal Article] 構造生物学2.0としての分子動力学シミュレーション:創薬応用への道2019
- Author(s)
  山下雄史
- Journal Title
  
  月刊「細胞」(The Cell)
  
  Volume: 51 Pages: 606-607
- Data Source
  KAKENHI-PROJECT-18K05025
[Journal Article] 構造生物学2.0としての分子動力学シミュレーション：創薬応用への道2019
- Author(s)
  山下雄史
- Journal Title
  
  月刊「細胞」(The Cell)
  
  Volume: 51 Pages: 606-607
- Data Source
  KAKENHI-PROJECT-15KT0103
[Journal Article] Modified AMBER force-field (FUJI) parameters for sulfated and phosphorylated tyrosine residues: Development and application to CCR5-derived peptide systems2019
- Author(s)
  Yamashita Takefumi, Okajima Ryo, Miyanabe Kazuhiro, Tsumoto Kouhei
- Journal Title
  
  AIP Conf. Proc.
  
  Volume: 2186 Pages: 030013-030013
- DOI
  10.1063/1.5137924
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16KT0050, KAKENHI-PROJECT-18K05025, KAKENHI-PROJECT-15H05752, KAKENHI-PROJECT-15KT0103
[Journal Article] 抗体医薬品設計に IT 革命を: 理論と計算による挑戦2019
- Author(s)
  山下雄史
- Journal Title
  
  月刊「細胞」(The Cell)
  
  Volume: 51 Pages: 344-347
- Data Source
  KAKENHI-PROJECT-18K05025
[Journal Article] 構造生物学2.0としての分子動力学シミュレーション：創薬応用への道 Molecular Dynamics Simulations as Structural Biology 2.0: Application to Drug Design2019
- Author(s)
  山下雄史
- Journal Title
  
  月刊「細胞」(The Cell)
  
  Volume: 51(12) Pages: 606-607
- Data Source
  KAKENHI-PROJECT-16KT0050
[Journal Article] Toward rational antibody design: recent advancements in molecular dynamics simulations2018
- Author(s)
  T. Yamashita
- Journal Title
  
  Int. Immunol.
  
  Volume: 30 Issue: 4 Pages: 133-140
- DOI
  10.1093/intimm/dxx077
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-15KT0103, KAKENHI-PROJECT-15H05752
[Journal Article] Liquid Structures Characterized by a Combination of the Persistent Homology Analysis and Molecular Dynamics Simulation2018
- Author(s)
  K. Sasaki, R. Okajima, and T. Yamashita
- Journal Title
  
  AIP Conf. Proc.
  
  Volume: 2040 Pages: 020014-020014
- DOI
  10.1063/1.5079057
- Open Access
- Data Source
  KAKENHI-PROJECT-15KT0103
[Journal Article] Tyrosine sulfation restricts the conformational ensemble of a flexible peptide, strengthening the binding affinity for an antibody2018
- Author(s)
  K. Miyanabe, T. Yamashita, Y. Abe, H. Akiba, Y. Takamatsu, M. Nakakido, T. Hamakubo, T. Ueda, JMM. Caaveiro, and K. Tsumoto
- Journal Title
  
  Biochemistry
  
  Volume: 57 Issue: 28 Pages: 4177-4185
- DOI
  10.1021/acs.biochem.8b00592
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15KT0103, KAKENHI-PROJECT-15H05752, KAKENHI-PROJECT-16H02420, KAKENHI-PROJECT-17H06109
[Journal Article] Efficiency Strategy for Peptide Design: a Comparative Study on All-atom, Coarse-grained, and Machine Learning Approaches2018
- Author(s)
  T. Yamashita, R. Okajima, and N. Shoji
- Journal Title
  
  AIP Conf. Proc.
  
  Volume: 2040 Pages: 020014-020014
- DOI
  10.1063/1.5079056
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-15KT0103, KAKENHI-PROJECT-15H05752
[Journal Article] Multiplicity in Long Noncoding RNA Biomedical Sciences2018
- Author(s)
  3.R. Kurokawa, R. Komiya, T. Oyoshi, Y. Matsuno, H. Tani, M. Katahira, K. Hitachi, Y. Iwashita, T. Yamashita, K. Kondo, R. Yoneda, Y. Yamaoki, N. Ueda, T. Mashima, N. Kobayashi, T. Nagata, A. Kiyoishi, M. Miyake, F. Kano, M. Murata1, N. Hamad, K. Sasaki, N. Shoji
- Journal Title
  
  Biomedical Sciences
  
  Volume: 4 Issue: 2 Pages: 18-23
- DOI
  10.11648/j.bs.20180402.11
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-15KT0103, KAKENHI-PROJECT-17K05930, KAKENHI-PROJECT-17K08646, KAKENHI-PROJECT-18K05025, KAKENHI-PUBLICLY-17H05608, KAKENHI-PROJECT-15H05752, KAKENHI-PROJECT-18K14636, KAKENHI-PROJECT-17K14515
[Journal Article] An ensemble docking calculation of lysozyme and HyHEL-10: Insight into the binding mechanism2017
- Author(s)
  Yamashita Takefumi、Takamatsu Yuichiro
- Journal Title
  
  AIP Conf. Proc.
  
  Volume: 1906 Pages: 030022-030022
- DOI
  10.1063/1.5012301
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15KT0103
[Journal Article] Plasma Irradiation Effects to Intra-Abdominal Organ Compared with Adhesion Mouse Model2017
- Author(s)
  K. Soda, H. Yamashita, K. Chang, T. Kawamura, T. Hamakubo and N. Shimizu
- Journal Title
  
  Plasma Medicine
  
  Volume: 印刷中
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-25220205
[Journal Article] n Ensemble Docking Calculation of Lysozyme and HyHEL-10: Insight into the Binding Mechanism2017
- Author(s)
  T. Yamashita and Y. Takamatsu,
- Journal Title
  
  AIP Conf. Proc.
  
  Volume: 1906 Pages: 030022-030022
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15H05752
[Journal Article] Molecular dynamics analysis to evaluate docking pose prediction2016
- Author(s)
  Takako Sakano, Md. Iqbal Mahmood, Takefumi Yamashita*, and Hideaki Fujitani
- Journal Title
  
  Biophysics and Physicobiology
  
  Volume: 13 Issue: 0 Pages: 181-194
- DOI
  10.2142/biophysico.13.0_181
- NAID
  130005165376
- ISSN
  2189-4779
- Language
  English
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-15H05752, KAKENHI-PROJECT-15KT0103
[Journal Article] Towards Physical Understanding of Molecular Recognition in the Cell: Recent Evolution of Molecular Dynamics Techniques and Free Energy Theories2016
- Author(s)
  Takefumi Yamashita
- Journal Title
  
  Biomedical Sciences
  
  Volume: 2 Pages: 34-47
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-15H05752
[Journal Article] On the Accurate Molecular Dynamics Analysis of Biological Molecules2016
- Author(s)
  T. Yamashita
- Journal Title
  
  AIP Conf. Proc.
  
  Volume: 1790 Pages: 020026-020026
- DOI
  10.1063/1.4968652
- Peer Reviewed / Acknowledgement Compliant / Open Access
- Data Source
  KAKENHI-PROJECT-15KT0103
[Journal Article] Towards Physical Understanding of Molecular Recognition in the Cell: Recent Evolution of Molecular Dynamics Techniques and Free Energy Theories2016
- Author(s)
  T. Yamashita
- Journal Title
  
  Biomedical Sciences
  
  Volume: 2 Pages: 34-47
- Peer Reviewed / Acknowledgement Compliant / Open Access
- Data Source
  KAKENHI-PROJECT-15KT0103
[Journal Article] Structural features of interfacial tyrosine residue in ROBO1 fibronectin domain-antibody complex: Crystallographic, thermodynamic, and molecular dynamic analyses.2015
- Author(s)
  Nakayama T, Mizohata E, Yamashita T, Nagatoishi S, Nakakido M, Iwanari H, Mochizuki Y, Kado Y, Yokota Y, Satoh R, Tsumoto K, Fujitani H, Kodama T, Hamakubo T, Inoue T.
- Journal Title
  
  Protein Sci
  
  Volume: 24 Issue: 3 Pages: 328-340
- DOI
  10.1002/pro.2619
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-24108007, KAKENHI-PROJECT-25220205
[Journal Article] Human mannose-binding lectin 2 is directly regulated by peroxisome proliferator-activated receptors (PPARs) via a peroxisome proliferator responsive element2013
- Author(s)
  Tachibana K, Takeuchi K, Inada H, Sugimoto K, Ishimoto K, Yamashita M, Maegawa T, Yamasaki D, Osada S, Tanaka T, Rakug H, Hamakubo T, Sakai J, Kodama T, Doi T
- Journal Title
  
  The Journal of Biochemistry
  
  Volume: 154 (3) Issue: 3 Pages: 265-73
- DOI
  10.1093/jb/mvt050
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22229009, KAKENHI-PROJECT-23790364, KAKENHI-PUBLICLY-24116507, KAKENHI-PROJECT-24650442, KAKENHI-PROJECT-25220205
[Presentation] 結合自由エネルギーの定量的予測と分子設計のための構造モチーフ探索2022
- Author(s)
  山下雄史
- Organizer
  CBI学会第432回講演会「結合自由エネルギー計算は創薬研究戦略を変えるか」
- Invited
- Data Source
  KAKENHI-PROJECT-18K05025
[Presentation] Molecular Dynamics Simulation for Biological and Material polymers2022
- Author(s)
  Takefumi Yamashita
- Organizer
  International Congress on Pure & Applied Chemistry (ICPAC) 2022
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K03482
[Presentation] MDシミュレーションで考える抗原-抗体界面における塩橋の役割：合理的な抗体設計に向けて2022
- Author(s)
  山下雄史
- Organizer
  日本蛋白質科学会学会年会
- Invited
- Data Source
  KAKENHI-PROJECT-18K05025
[Presentation] Properties of the Protein-Protein Interface Revealed by Molecular dynamics Simulations2022
- Author(s)
  Takefumi Yamashita
- Organizer
  18th International Conference of Computational Methods in Sciences and Engineering (QS symposium of ICCMSE 2022)
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K03482
[Presentation] Properties of the Protein-Protein Interface Revealed by Molecular dynamics Simulations2022
- Author(s)
  Takefumi Yamashita
- Organizer
  18th International Conference of Computational Methods in Sciences and Engineering (QS symposium of ICCMSE 2022)
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18K05025
[Presentation] Molecular Dynamics Simulation for Biological and Material polymers2022
- Author(s)
  Takefumi Yamashita
- Organizer
  International Congress on Pure & Applied Chemistry (ICPAC) 2022
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18K05025
[Presentation] MDシミュレーションで考える抗原-抗体界面：合理的な抗体医薬品設計に向けて A molecular dynamics study on the antigen-antibody interface: Toward rational antibody drug design2022
- Author(s)
  山下雄史
- Organizer
  日本生物物理学会年会
- Invited
- Data Source
  KAKENHI-PROJECT-18K05025
[Presentation] 抗原-抗体界面の塩橋の安定性とその役割に関する理論的研究（A theoretical study on the salt bridge stability on the antigen-antibody interface and its effect）2021
- Author(s)
  山下雄史
- Organizer
  日本生物物理学会
- Data Source
  KAKENHI-PROJECT-18K05025
[Presentation] 分子動力学シミュレーションを用いた抗体設計の可能性2021
- Author(s)
  山下雄史
- Organizer
  構造活性フォーラム２０２１：次期スーパーコンピュータ『富岳』時代の計算創薬
- Invited
- Data Source
  KAKENHI-PROJECT-18K05025
[Presentation] Dynamical boundaries for the isomerization reaction HCN ←→ CNH in the presence of a buffer molecule2021
- Author(s)
  Shinnosuke KAWAI, and Takefumi YAMASHITA
- Organizer
  ICCMSE 2021 (17th International Conference of Computational Methods in Sciences and Engineering)，Galaxy Hotel, Heraklion, Crete, Greece
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16KT0050
[Presentation] Salt Bridge Stability in the Antigen-Antibody Interface and its Impact on the Binding Affinity: Insight from Molecular Dynamics Simulations2021
- Author(s)
  Takefumi Yamashita
- Organizer
  17th International Conference of Computational Methods in Sciences and Engineering (QS symposium of ICCMSE 2021)
- Invited
- Data Source
  KAKENHI-PROJECT-18K05025
[Presentation] Molecular dynamics simulations reveal the protein-protein interaction mechanism2020
- Author(s)
  Takefumi Yamashita
- Organizer
  16th International Conference of Computational Methods in Sciences and Engineering (CC symposium of ICCMSE 2020)
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18K05025
[Presentation] 分子動力学シミュレーションを用いた抗体設計の可能性: ”動き”に含まれる親和性のエッセンス2020
- Author(s)
  山下雄史
- Organizer
  第414回CBI学会講演会「実験と計算化学を用いた抗体医薬設計の最近の進展」
- Invited
- Data Source
  KAKENHI-PROJECT-15H05752
[Presentation] 分子動力学シミュレーションを用いた抗体設計の可能性: ”動き”に含まれる親和性のエッセンス2020
- Author(s)
  山下雄史
- Organizer
  CBI学会講演会「実験と計算化学を用いた抗体医薬設計の最近の進展」
- Invited
- Data Source
  KAKENHI-PROJECT-15KT0103
[Presentation] 分子動力学シミュレーションを用いた抗体設計の可能性: ”動き”に含まれる親和性のエッセンス2020
- Author(s)
  山下雄史
- Organizer
  CBI学会講演会「実験と計算化学を用いた抗体医薬設計の最近の進展」
- Invited
- Data Source
  KAKENHI-PROJECT-18K05025
[Presentation] 抗原-抗体界面における塩橋安定性の理論的解析2020
- Author(s)
  山下雄史
- Organizer
  第1回生体分子シミュレーション・モデリング研究会
- Data Source
  KAKENHI-PROJECT-18K05025
[Presentation] Effect of the interfacial water molecule on the antigen-antibody interaction: A molecular dynamics study2019
- Author(s)
  Takefumi Yamashita
- Organizer
  15th International Conference of Computational Methods in Sciences and Engineering (CC symposium of ICCMSE 2019)
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18K05025
[Presentation] Effects of alanine substitution on antigen-antibody interaction: A molecular dynamics study2019
- Author(s)
  Takefumi Yamashita
- Organizer
  International Congress on Pure & Applied Chemistry (ICPAC) Yangon 2019
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15H05752
[Presentation] Mechanism of antibody-affinity enhancement through alanine-substitution2019
- Author(s)
  山下雄史
- Organizer
  日本生物物理学会年会（Symposium “New horizon of in-silico drug discovery toward launching post-K computer”）
- Invited
- Data Source
  KAKENHI-PROJECT-15KT0103
[Presentation] 分子動力学シミュレーションでせまるタンパク質間相互作用 “Molecular dynamics simulations reveal the protein-protein interaction mechanism”2019
- Author(s)
  山下雄史
- Organizer
  シンポジウム「化学反応経路探索のニューフロンティア2019」
- Invited
- Data Source
  KAKENHI-PROJECT-15H05752
[Presentation] Effects of alanine substitution on antigen-antibody interaction: A molecular dynamics study2019
- Author(s)
  Takefumi Yamashita
- Organizer
  International Congress on Pure & Applied Chemistry (ICPAC) Yangon 2019
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15KT0103
[Presentation] Effect of the interfacial water molecule on the antigen-antibody interaction: A molecular dynamics study2019
- Author(s)
  Takefumi Yamashita
- Organizer
  15th International Conference of Computational Methods in Sciences and Engineering (CC symposium of ICCMSE 2019)
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15KT0103
[Presentation] Effects of alanine substitution on antigen-antibody interaction: A molecular dynamics study2019
- Author(s)
  Takefumi Yamashita
- Organizer
  International Congress on Pure & Applied Chemistry (ICPAC) Yangon 2019(招待講演)(国際学会)
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18K05025
[Presentation] 高精度な分子動力学シミュレーションの為の分子間相互作用モデルの改良2019
- Author(s)
  佐々木皓平・山下雄史
- Organizer
  日本化学会年会
- Data Source
  KAKENHI-PROJECT-15H05752
[Presentation] Effect of the interfacial water molecule on the antigen-antibody interaction: A molecular dynamics study2019
- Author(s)
  Takefumi Yamashita
- Organizer
  15th International Conference of Computational Methods in Sciences and Engineering (CC symposium of ICCMSE 2019)
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15H05752
[Presentation] 粗視化モデルを用いたエポキシ樹脂の物性値と分子構造の関係性についての解析2019
- Author(s)
  庄司直幸・山下雄史
- Organizer
  日本化学会年会
- Data Source
  KAKENHI-PROJECT-15H05752
[Presentation] 分子動力学シミュレーションでせまるタンパク質間相互作用2019
- Author(s)
  山下雄史
- Organizer
  シンポジウム「化学反応経路探索のニューフロンティア2019」
- Invited
- Data Source
  KAKENHI-PROJECT-18K05025
[Presentation] 分子動力学シミュレーションでせまるタンパク質間相互作用2019
- Author(s)
  山下雄史
- Organizer
  シンポジウム「化学反応経路探索のニューフロンティア2019」
- Invited
- Data Source
  KAKENHI-PROJECT-15KT0103
[Presentation] アラニン置換による抗体親和性の向上のメカニズム“Mechanism of antibody-affinity enhancement through alanine-substitution”2019
- Author(s)
  山下雄史
- Organizer
  日本生物物理学会年会
- Invited
- Data Source
  KAKENHI-PROJECT-15H05752
[Presentation] Mechanism of antibody-affinity enhancement through alanine-substitution2019
- Author(s)
  山下雄史
- Organizer
  日本生物物理学会年会(Symposium “New horizon of in-silico drug discovery toward launching post-K computer”)
- Invited
- Data Source
  KAKENHI-PROJECT-18K05025
[Presentation] 粗視化モデルにおけるエポキシ樹脂の分子構造と物性値の関係2018
- Author(s)
  庄司直幸・山下雄史
- Organizer
  分子シミュレーション討論会
- Data Source
  KAKENHI-PROJECT-15H05752
[Presentation] 高精度な分子動力学計算のための静電相互作用パラメータの検討2018
- Author(s)
  佐々木皓平・山下雄史
- Organizer
  日本化学会年会
- Data Source
  KAKENHI-PROJECT-15H05752
[Presentation] 粗視化モデルにおけるエポキシ樹脂のネットワーク構造と物性値の関係2018
- Author(s)
  庄司直幸・山下雄史
- Organizer
  高分子討論会
- Data Source
  KAKENHI-PROJECT-15H05752
[Presentation] Molecular dynamics in the antibody-antigen recognition2018
- Author(s)
  Takefumi Yamashita
- Organizer
  Symposium on Eukaryotic Regulatory Biology in honor of M. Geoffrey Rosenfeld
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15KT0103
[Presentation] Effect of interface structure on the binding affinity of proteins: A molecular dynamics study2018
- Author(s)
  Takefumi Yamashita
- Organizer
  IMS symposium "Water at interfaces 2018"
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15KT0103
[Presentation] Effect of interface structure on the binding affinity of proteins: A molecular dynamics study2018
- Author(s)
  Takefumi Yamashita
- Organizer
  IMS symposium "Water at interfaces 2018"
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18K05025
[Presentation] Structural effects on the antigen-antibody interaction: Insight from molecular dynamics simulations of biopolymers2018
- Author(s)
  Takefumi Yamashita
- Organizer
  14th International Conference of Computational Methods in Sciences and Engineering (CC symposium of ICCMSE 2017)(Thessaloniki, Greece / Invited lecture)
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15KT0103
[Presentation] 分子動力学シミュレーションによる材料高分子の研究：熱硬化性樹脂の高精度モデリング2018
- Author(s)
  山下雄史
- Organizer
  第８回 NTChem ワークショップ
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15KT0103
[Presentation] 分子動力学計算を用いた抗原抗体界面に存在する塩橋の安定性を決定する要因の研究2018
- Author(s)
  岡島亮，山下雄史
- Organizer
  分子科学討論会
- Data Source
  KAKENHI-PROJECT-15H05752
[Presentation] Molecular dynamics in the antibody-antigen recognition2018
- Author(s)
  Takefumi Yamashita
- Organizer
  Symposium on Eukaryotic Regulatory Biology in honor of M. Geoffrey Rosenfeld
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18K05025
[Presentation] 分子動力学計算を用いた抗原抗体界面に存在する塩橋の安定性を決定する要因の研究2018
- Author(s)
  岡島亮、山下雄史
- Organizer
  分子科学討論会
- Data Source
  KAKENHI-PROJECT-18K05025
[Presentation] A Molecular Dynamics Study on Antigen-Antibody Recognition2017
- Author(s)
  Takefumi Yamashita,
- Organizer
  13th International Conference of Computational Methods in Sciences and Engineering, Greece
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15H05752
[Presentation] Molecular Dynamics Analysis of Protein Complex Structures2017
- Author(s)
  Takefumi Yamashita
- Organizer
  10th International Conference on Computational Physics (ICCP10)
- Place of Presentation
  Macau, China
- Year and Date
  2017-01-16
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15KT0103
[Presentation] A Molecular Dynamics Study on Antigen-Antibody Recognition2017
- Author(s)
  Takefumi Yamashita
- Organizer
  13th International Conference of Computational Methods in Sciences and Engineering (CC symposium of ICCMSE 2017)(Thessaloniki, Greece / Invited lecture)
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15KT0103
[Presentation] 分子動力学シミュレーションによるタンパク質の分子認識の研究：分子デザインへの挑戦2017
- Author(s)
  山下雄史
- Organizer
  量子系分子科学セミナー（理化学研究所計算科学研究機構）
- Data Source
  KAKENHI-PROJECT-15H05752
[Presentation] 分子動力学シミュレーションによるタンパク質の分子認識の研究：分子デザインへの挑戦2017
- Author(s)
  山下雄史
- Organizer
  量子系分子科学セミナー（理化学研究所計算科学研究機構）
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15KT0103
[Presentation] 分子動力学計算による抗原抗体複合体の形成過程の研究2017
- Author(s)
  山下雄史, 高松佑一郎
- Organizer
  日本化学会春季年会
- Place of Presentation
  慶応義塾大学（神奈川県横浜市）
- Year and Date
  2017-03-16
- Data Source
  KAKENHI-PROJECT-15KT0103
[Presentation] 分子動力学計算による抗原と抗体の結合過程の研究2017
- Author(s)
  山下雄史・高松佑一郎
- Organizer
  分子科学討論会
- Data Source
  KAKENHI-PROJECT-15KT0103
[Presentation] ヒストンの血管内皮細胞障害を阻害するPTX3の凝集パターン解析2017
- Author(s)
  早田敬太、中木戸誠、太期健二、高松佑一郎、山下雄史、岩成宏子、津本浩平、浜窪隆雄
- Organizer
  2017年度生命科学系会合同年次大会
- Data Source
  KAKENHI-PROJECT-25220205
[Presentation] Molecular Environment effects on the protein structure: Molecular dynamics studies on the antigen-antibody interface2017
- Author(s)
  Takefumi Yamashita
- Organizer
  生物物理学会(Symposium: Molecular-Level Analysis of Environment Effect toward Tuning of Protein Structure and Function)
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15KT0103
[Presentation] 分子動力学シミュレーションによる生体高分子の研究：RNAへの展開の現状と可能性2017
- Author(s)
  山下雄史
- Organizer
  2017年度生命科学系学会合同年次大会(ConBio2017)ワークショップ
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15KT0103
[Presentation] Molecular Dynamics Analysis of Protein Complex Structures2017
- Author(s)
  Takefumi Yamashita
- Organizer
  10th International Conference on Computational Physics
- Place of Presentation
  Macau, China
- Year and Date
  2017-01-16
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15H05752
[Presentation] 生体分子のダイナミクスと機能：分子動力学シミュレーションの非コードRNA研究ツールとしての可能性2017
- Author(s)
  山下雄史
- Organizer
  一般財団法人バイオインダストリー協会主催"未来へのバイオ技術" 勉強会「長鎖非コードRNA研究の進歩と可能性」
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15KT0103
[Presentation] On Quantitative Understanding on Antigen-Antibody Interaction through All-atom Molecular Dynamics Simulations2017
- Author(s)
  Takefumi Yamashita
- Organizer
  3rd Symposium on Biophysics Postgraduate Research in Hong Kong
- Place of Presentation
  Hong Kong, China
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15H05752
[Presentation] On Quantitative Understanding on Antigen-Antibody Interaction through All-atom Molecular Dynamics Simulations2017
- Author(s)
  Takefumi Yamashita
- Organizer
  3rd Symposium on Biophysics Postgraduate Research in Hong Kong
- Place of Presentation
  Hong Kong, China
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15KT0103
[Presentation] Advancement and challenge in the all-atom molecular dynamics simulation for biomolecular systems2016
- Author(s)
  Takefumi Yamashita
- Organizer
  第３９回日本分子生物学会年会
- Place of Presentation
  パシフィコ横浜（神奈川県横浜市）
- Year and Date
  2016-11-30
- Invited
- Data Source
  KAKENHI-PROJECT-15KT0103
[Presentation] Molecular Dynamics Simulation of Biomolecules: Accuracy Improvement and Computational Conditions2016
- Author(s)
  Takefumi Yamashita
- Organizer
  12th International Conference of Computational Methods in Sciences and Engineering (CC symposium of ICCMSE 2016)
- Place of Presentation
  Athens (Greek)
- Year and Date
  2016-03-20
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15KT0103
[Presentation] 分子動力学シミュレーションと蛋白質-小分子相互作用2016
- Author(s)
  山下雄史
- Organizer
  第８９回薬理学会年会　シンポジウム「計算科学的アプローチによる薬理学研究の新展開」
- Place of Presentation
  横浜
- Year and Date
  2016-03-11
- Invited
- Data Source
  KAKENHI-PROJECT-15KT0103
[Presentation] The Establishment of Peritoneal Adhesion Mouse Model For The Plasma Medicine2015
- Author(s)
  Keita Soda,Hiroharu Yamashita,Kyungho Chang, Nobuyuki Shimizu,Takao Hamakubo
- Organizer
  The 2nd international Workshop on Plasma for Cancer Treatmant
- Place of Presentation
  名古屋
- Year and Date
  2015-03-16
- Data Source
  KAKENHI-PROJECT-25220205
[Presentation] 熱力学的相互作用解析と分子動力学シミュレーションによる抗体の親和性向上のメカニズムの研究2013
- Author(s)
  渡部貴大,長門石曉,山下雄史,中山泰亮,溝端栄一,浜窪隆雄,井上豪,津本浩平,児玉龍彦,藤谷秀章
- Organizer
  第36回日本分子生物学会
- Place of Presentation
  神戸
- Year and Date
  2013-12-03
- Data Source
  KAKENHI-PROJECT-25220205
[Presentation] 創傷治癒における炎症反応の分子メカニズム解析2013
- Author(s)
  早田　敬太、太期　健二、川村　猛、山下　裕玄、張　京浩、榊田　創、池原　譲、清水　伸幸、浜窪　隆雄
- Organizer
  名古屋プラズマ医療科学の創成第二回公開シンポジウム
- Place of Presentation
  名古屋
- Year and Date
  2013-09-28
- Data Source
  KAKENHI-PROJECT-25220205
[]

1. Takatsuka Kazuo (70154797)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
2. Kawai Shinnosuke (90624065)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
3. HAMAKUBO TAKAO (90198797)

# of Collaborated Projects: 1 results

# of Collaborated Products: 6 results
4. Fujitani Hideaki (50417151)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
5. Nagatoishi Satoru (30550248)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
6. Washiyama Kohshin (80313675)

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7. 児玉大樹 (40466826)

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8. 高橋聡 (20456180)

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11. 川村猛 (70306835)

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12. 篠田恵子 (80646951)

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13. 津本浩平 (90271866)

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22. 山下裕玄

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23. 酒井寿郎

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Takefumi Yamashita 山下 雄史

Yamashita Takefumi 山下 雄史

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高分子アモルファスのマルチスケールシミュレーション技術の基礎理論の確立と実践Principal Investigator

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１細胞計測に基づく細胞モデルとそれに基づく形態形成の理論の開発Principal Investigator

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Optimization of pretargeted alpha therapy for multiple types of cancer

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Dynamics of protein-protein interface: Development of analysis methods based on machine learning and MD simulationPrincipal Investigator

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Theoretical elucidation of dynamical solvent effects in controling chemical reactions

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Development of Molecular Dynamics Classification Theories for Life Science and Drug DesignPrincipal Investigator

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Nonadiabatic Electron Dynamics in Chemistry of Charge Separation, Proton Transfer, Electron Transmission, and Huge Electronic-State Fluctuation

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Dynamics of Molecular Pattern Recognition in Protein Interaction

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[Journal Article] Effect of N343 glycosylation and N501Y mutation on the SARS-CoV-2 spike protein: Modeling and MD Simulations2022

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[Journal Article] Singular spectrum transformation for detecting molecular motion mode change of protein systems2021

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[Journal Article] 抗体医薬品設計に IT 革命を: 理論と計算による挑戦2019

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[Journal Article] A SNP in a Steroidogenic Enzyme Is Associated with Phenotypic Sex in Seriola Fishes2019

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[Journal Article] Convergence in LINE-1 nucleotide variations can benefit redundantly forming triplexes with lncRNA in mammalian X-chromosome inactivation2019

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[Journal Article] 構造生物学2.0としての分子動力学シミュレーション:創薬応用への道2019

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Takefumi Yamashita 山下雄史

Yamashita Takefumi 山下雄史