Sakuraba Shun 櫻庭俊

Researcher Number	90647380
Other IDs
Affiliation (Current)	2025: 国立研究開発法人量子科学技術研究開発機構, 量子生命科学研究所, 上席研究員
Affiliation (based on the past Project Information) *help	2021 – 2024: 国立研究開発法人量子科学技術研究開発機構, 量子生命科学研究所, 主幹研究員 2020 – 2021: 国立研究開発法人量子科学技術研究開発機構, 量子生命科学研究所, 主任研究員 2018 – 2020: 国立研究開発法人量子科学技術研究開発機構, 量子生命科学領域, 主任研究員(任常) 2018: 国立研究開発法人量子科学技術研究開発機構, 関西光科学研究所量子生命科学研究部, 主任研究員(任常) 2016 – 2017: 東京大学, 大学院新領域創成科学研究科, 特任助教
Review Section/Research Field	Principal Investigator Complex systems / Medium-sized Section 13:Condensed matter physics and related fields / Biological physics/Chemical physics/Soft matter physics Except Principal Investigator Transformative Research Areas, Section (III) / Medium-sized Section 62:Applied informatics and related fields / System genome science
Keywords	Principal Investigator 分子動力学法 / 分子動力学 / 分子動力学シミュレーション / 拡張アンサンブル / 分子シミュレーション / 自由エネルギー計算 / 力場 / タンパク質 / ハイブリッドモンテカルロ法 / タンパク質構造 … More / 構造サンプリング / 主成分分析 / 質量テンソル分子動力学法 / 機械学習 / 敵対的生成ネットワーク / 生成モデル / パラメータサーチ / 記号回帰 / 活性化エネルギー / 発動分子 / 拡張アンサンブル法 / 経験的原子価結合法 / 化学物理 / リボ核酸 / 古典分子動力学シミュレーション / 零多重極子和法 / 二次構造予測 / 修飾核酸 / N6-メチルアデニン / イノシン / 力場パラメータ / 修飾核酸塩基 / RNA修飾 / RNA … More Except Principal Investigator 分子動力学 / RNA２次構造 / 修飾塩基 / 種間障壁 / 自他識別 / 受精前障壁 / MDシミュレーション / 有機化学 / タンパク質間相互作用 / 生殖 / 植物 / mRNA翻訳 / 翻訳効率 / RNA修飾塩基 / 異分野技術融合 / 国際活動支援 / 異分野コア技術群支援 / ゲノム動態 / 繁殖適応戦略 / 両性花 / エピトランスクリプトーム解析 / エピとランスクリプトーム解析 / ＲＮＡ2次構造 / エヒトランスプリクトーム / RNA2次構造 / エネルギーパラメタ / バイオインフォマティクス / エピトランスクリプトーム Less

Genomic dynamics underlying the plastic hermaphroditism in plants: the basis of exploratory reproductive adaptations
- Principal Investigator
  
  赤木剛士
- Project Period (FY)
  2022 – 2026
- Research Category
  
  Grant-in-Aid for Transformative Research Areas (A)
- Review Section
  
  Transformative Research Areas, Section (III)
- Research Institution
  Okayama University
Molecular dynamic mechanism of the sexual selection core in the plant hermaphroditism
- Principal Investigator
  
  藤井壮太
- Project Period (FY)
  2022 – 2026
- Research Category
  
  Grant-in-Aid for Transformative Research Areas (A)
- Review Section
  
  Transformative Research Areas, Section (III)
- Research Institution
  The University of Tokyo
修飾塩基を持つRNAの情報解析基盤技術の開発
- Principal Investigator
  
  浅井潔
- Project Period (FY)
  2021 – 2023
- Research Category
  
  Grant-in-Aid for Scientific Research (A)
- Review Section
  
  Medium-sized Section 62:Applied informatics and related fields
- Research Institution
  The University of Tokyo
Distribution Matching Principle for Machine Learning Based Molecular SimulationPrincipal Investigator
- Principal Investigator
  
  Sakuraba Shun
- Project Period (FY)
  2020 – 2023
- Research Category
  
  Grant-in-Aid for Challenging Research (Exploratory)
- Review Section
  
  Medium-sized Section 13:Condensed matter physics and related fields
- Research Institution
  National Institutes for Quantum Science and Technology
Quick sampling of protein large conformational changesPrincipal Investigator
- Principal Investigator
  
  櫻庭俊
- Project Period (FY)
  2020 – 2021
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Review Section
  
  Complex systems
- Research Institution
  National Institutes for Quantum Science and Technology
Empirical valence bond method combined with extended ensemble simulations and its application to molecular enginesPrincipal Investigator
- Principal Investigator
  
  櫻庭俊
- Project Period (FY)
  2019 – 2020
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Review Section
  
  Complex systems
- Research Institution
  National Institutes for Quantum and Radiological Science and Technology
Force fields for the molecular dynamics of modified nucleic acidsPrincipal Investigator
- Principal Investigator
  
  Sakuraba Shun
- Project Period (FY)
  2016 – 2019
- Research Category
  
  Grant-in-Aid for Young Scientists (B)
- Research Field
  
  Biological physics/Chemical physics/Soft matter physics
- Research Institution
  National Institutes for Quantum and Radiological Science and Technology
  The University of Tokyo
RNA informatics for epi-transcriptome analysis
- Principal Investigator
  
  Asai Kiyoshi
- Project Period (FY)
  2016 – 2018
- Research Category
  
  Grant-in-Aid for Scientific Research (A)
- Research Field
  
  System genome science
- Research Institution
  The University of Tokyo

All 2023 2022 2021 2020 2019 2018 2017 2016

All Journal Article Presentation Patent

[Journal Article] Prediction of Ciclesonide Binding Site on Middle-East Respiratory Syndrome Coronavirus Nsp15 Multimer by Molecular Dynamics Simulations2021
- Author(s)
  Sakuraba Shun, Kono Hidetoshi
- Journal Title
  
  chemrxiv
  
  Volume: -
- DOI
  10.26434/chemrxiv.13602731.v1
- Open Access
- Data Source
  KAKENHI-PUBLICLY-19H05410
[Journal Article] Modeling the SARS-CoV-2 nsp1-5’-UTR complex via the extended ensemble simulations2021
- Author(s)
  Sakuraba Shun, Xie Qilin, Kasahara Kota, Iwakiri Junichi, Kono Hidetoshi
- Journal Title
  
  bioRxiv
  
  Volume: -
- DOI
  10.1101/2021.02.24.432807
- Open Access
- Data Source
  KAKENHI-PUBLICLY-19H05410
[Journal Article] Free-Energy Calculation of Ribonucleic Inosines and Its Application to Nearest-Neighbor Parameters2020
- Author(s)
  Sakuraba Shun、Iwakiri Junichi、Hamada Michiaki、Kameda Tomoshi、Tsuji Genichiro、Kimura Yasuaki、Abe Hiroshi、Asai Kiyoshi
- Journal Title
  
  Journal of Chemical Theory and Computation
  
  Volume: 16 Issue: 9 Pages: 5923-5935
- DOI
  10.1021/acs.jctc.0c00270
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20K12041, KAKENHI-PUBLICLY-19H05410, KAKENHI-PROJECT-16H06279
[Journal Article] Performance Evaluation of the Zero-Multipole Summation Method in Modern Molecular Dynamics Software2018
- Author(s)
  Shun Sakuraba, Ikuo Fukuda
- Journal Title
  
  Journal of Computational Chemistry
  
  Volume: 印刷中 Issue: 20 Pages: 1551-1560
- DOI
  10.1002/jcc.25228
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16K17778
[Journal Article] Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities2018
- Author(s)
  Hagio Taichi、Sakuraba Shun、Iwakiri Junichi、Mori Ryota、Asai Kiyoshi
- Journal Title
  
  BMC Bioinformatics
  
  Volume: 19 Issue: Suppl 1 Pages: 38-38
- DOI
  10.1186/s12859-018-2018-4
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16K16143, KAKENHI-PROJECT-16K17778, KAKENHI-PROJECT-16H06279, KAKENHI-PROJECT-16H02484
[Journal Article] Enhanced Sampling of Molecular Dynamics Simulations of a Polyalanine Octapeptide: Effects of the Periodic Boundary Conditions on Peptide Conformation2018
- Author(s)
  Kasahara Kota、Sakuraba Shun、Fukuda Ikuo
- Journal Title
  
  The Journal of Physical Chemistry B
  
  Volume: 122 Issue: 9 Pages: 2495-2503
- DOI
  10.1021/acs.jpcb.7b10830
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17K05143, KAKENHI-PROJECT-16K17778, KAKENHI-PROJECT-16K18526
[Journal Article] Estimating energy parameters for RNA secondary structure predictions using both experimental and computational data2018
- Author(s)
  Shimpei Nishida, Shun Sakuraba, Kiyoshi Asai, Michiaki Hamada
- Journal Title
  
  IEEE/ACM Transactions on Computational Biology and Bioinformatics
  
  Volume: 印刷中
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16K17778
[Journal Article] Estimating energy parameters for RNA secondary structure predictions using both experimental and computational data2018
- Author(s)
  Shimpei Nishida, Shun Sakuraba, Kiyoshi Asai, and Michiaki Hamada
- Journal Title
  
  IEEE/ACM Transactions on Computational Biology and Bioinformatics
  
  Volume: - Issue: 5 Pages: 1645-1655
- DOI
  10.1109/tcbb.2018.2813388
- Description
  in press
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16H06279, KAKENHI-PROJECT-16H05879, KAKENHI-PROJECT-16H02484
[Patent] 新規ヒトインターロイキンー１８変異体及びその用途2021
- Inventor(s)
  田中義正, 櫻庭俊
- Industrial Property Rights Holder
  長崎大、神戸医療産業機構、量研機構
- Industrial Property Rights Type
  特許
- Industrial Property Number
  2021-019418
- Filing Date
  2021
- Data Source
  KAKENHI-PUBLICLY-19H05410
[Presentation] 多腕banditによるタンパク質安定化提案の成功と失敗2023
- Author(s)
  櫻庭俊
- Organizer
  CPS研究会2023年勉強会
- Data Source
  KAKENHI-PROJECT-20K20907
[Presentation] 記号回帰による軽量な相互作用関数の探索2023
- Author(s)
  櫻庭俊
- Organizer
  第37回分子シミュレーション討論会
- Data Source
  KAKENHI-PROJECT-20K20907
[Presentation] 記号回帰による量子相互作用模倣2022
- Author(s)
  櫻庭俊
- Organizer
  量子生命科学会第4回大会
- Data Source
  KAKENHI-PROJECT-20K20907
[Presentation] 記号回帰による「都合の良い」ポテンシャル関数の探索2022
- Author(s)
  櫻庭俊
- Organizer
  第36回　分子シミュレーション討論会
- Data Source
  KAKENHI-PROJECT-20K20907
[Presentation] モデリング構造に基づく経験的原子価結合法による酵素反応活性化エネルギー予測2021
- Author(s)
  櫻庭　俊
- Organizer
  発動分子科学　第五回領域会議
- Data Source
  KAKENHI-PUBLICLY-19H05410
[Presentation] SARS-CoV-2 nsp1の自己認識機構をさぐる2021
- Author(s)
  櫻庭　俊
- Organizer
  計算タンパク質科学研究会第1回オンライン勉強会
- Data Source
  KAKENHI-PUBLICLY-19H05410
[Presentation] 経験的原子価結合法による酵素の活性化自由エネルギー計算2020
- Author(s)
  櫻庭　俊
- Organizer
  量子生命科学会第２回大会
- Data Source
  KAKENHI-PUBLICLY-19H05410
[Presentation] A COMPUTATIONAL STUDY OF FREE-ENERGY CHANGES UPON PROTEIN MUTATIONS2020
- Author(s)
  Shun Sakuraba
- Organizer
  2020 Biophysical Society Annual Meeting
- Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-19H05410
[Presentation] モデリング構造に基づく経験的原子価結合法による酵素反応活性化エネルギー予測2020
- Author(s)
  櫻庭　俊
- Organizer
  発動分子科学　第四回領域会議
- Data Source
  KAKENHI-PUBLICLY-19H05410
[Presentation] Stable Interdomain Interfaces of Heterochromatin Protein 1: Modeling all-atom Dinucleosome HP1 complex2019
- Author(s)
  Amarjeet Kumar, Shun Sakuraba, Atsushi Matsumoto, Hidetoshi Kono
- Organizer
  3rd QST International Symposium
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16K17778
[Presentation] Empirical Valence Bond Calculation of Triosephosphate Isomerase2019
- Author(s)
  Shun Sakuraba
- Organizer
  The 1st International Symposium on Molecular Engine
- Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-19H05410
[Presentation] FEP/REST法によるタンパク質変異体の自由エネルギー計算2019
- Author(s)
  櫻庭俊
- Organizer
  第33回分子シミュレーション討論会, 分子シミュレーション学会
- Data Source
  KAKENHI-PUBLICLY-19H05410
[Presentation] RNA nearest-neighbor parameters for inosine-cytosine pairs derived from a combined experiment-simulation approach2019
- Author(s)
  Shun Sakuraba, Junichi Iwakiri, Michiaki Hamada, Tomoshi Kameda, Genichiro Tsuji, Yasuaki Kimura, Hiroshi Abe, Kiyoshi Asai
- Organizer
  Annual Meeting of the Biophysical Society
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16K17778
[Presentation] FEP/RESTによるタンパク質の変異安定性予測2019
- Author(s)
  櫻庭　俊
- Organizer
  計算タンパク質科学研究会
- Data Source
  KAKENHI-PROJECT-16K17778
[Presentation] FEP/RESTによるタンパク質の変異安定性予測2019
- Author(s)
  櫻庭俊
- Organizer
  CPS研究会2019年勉強会
- Data Source
  KAKENHI-PUBLICLY-19H05410
[Presentation] FEP/REST法によるタンパク質変異体の自由エネルギー計算2019
- Author(s)
  櫻庭　俊
- Organizer
  第33回分子シミュレーション討論会
- Data Source
  KAKENHI-PROJECT-16K17778
[Presentation] Estimating energy parameters for RNA secondary structure predictions using both experimental and computational data2017
- Author(s)
  Shimpei Nishida, Shun Sakuraba, Kiyoshi Asai, Michiaki Hamada
- Organizer
  The 28th International Conference on Genome Informatics GIW/BIOINFO 2017
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16H02484
[Presentation] Capturing Alternative Secondary Structures of RNA by Decomposition of Base Pairing Probabilities2017
- Author(s)
  Taichi Hagio, Shun Sakuraba, Junichi Iwakiri, Ryota Mori and Kiyoshi Asai
- Organizer
  The 28th International Conference on Genome Informatics GIW/BIOINFO 2017
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16H02484
[Presentation] Predicting RNA-RNA duplex dimerization energy from the molecular dynamics simulation2016
- Author(s)
  Shun Sakuraba, Tomoshi Kameda and Kiyoshi Asai
- Organizer
  RNA2016
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16H02484

1. Asai Kiyoshi (30356357)

# of Collaborated Projects: 2 results

# of Collaborated Products: 4 results
2. 阿部洋 (80415067)

# of Collaborated Projects: 2 results

# of Collaborated Products: 0 results
3. 藤井壮太 (90716713)

# of Collaborated Projects: 2 results

# of Collaborated Products: 0 results
4. 草野修平 (80759291)

# of Collaborated Projects: 2 results

# of Collaborated Products: 0 results
5. 浜田道昭 (00596538)

# of Collaborated Projects: 1 results

# of Collaborated Products: 2 results
6. 亀田倫史 (40415774)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
7. 赤木剛士 (50611919)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
8. 木下哲 (60342630)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
9. 伊藤寿朗 (90517096)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
10. 榊原恵子 (90590000)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
11. 奥田哲弘 (90727702)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
12. 清水健太郎 (10742629)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
13. 井澤毅 (10263443)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
14. 白澤健太 (60527026)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
15. 渡辺正夫 (90240522)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
16. 内田誠一 (70315125)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
17. 遠藤真咲 (40546371)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
18. 小田原瑛美子 (40802054)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
19. 越阪部晃永 (70632107)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
20. 加藤義宣 (10869390)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
21. 岩切淳一

# of Collaborated Projects: 0 results

# of Collaborated Products: 2 results
22. 福田育夫

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
23. 位田隆一

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

Sakuraba Shun 櫻庭 俊

Research Projects

Research Products

Co-Researchers

Genomic dynamics underlying the plastic hermaphroditism in plants: the basis of exploratory reproductive adaptations

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Molecular dynamic mechanism of the sexual selection core in the plant hermaphroditism

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

修飾塩基を持つRNAの情報解析基盤技術の開発

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Distribution Matching Principle for Machine Learning Based Molecular SimulationPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Quick sampling of protein large conformational changesPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Empirical valence bond method combined with extended ensemble simulations and its application to molecular enginesPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Force fields for the molecular dynamics of modified nucleic acidsPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

RNA informatics for epi-transcriptome analysis

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

[Journal Article] Prediction of Ciclesonide Binding Site on Middle-East Respiratory Syndrome Coronavirus Nsp15 Multimer by Molecular Dynamics Simulations2021

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Modeling the SARS-CoV-2 nsp1-5’-UTR complex via the extended ensemble simulations2021

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Free-Energy Calculation of Ribonucleic Inosines and Its Application to Nearest-Neighbor Parameters2020

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Performance Evaluation of the Zero-Multipole Summation Method in Modern Molecular Dynamics Software2018

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities2018

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Enhanced Sampling of Molecular Dynamics Simulations of a Polyalanine Octapeptide: Effects of the Periodic Boundary Conditions on Peptide Conformation2018

Author(s)

Journal Title

Sakuraba Shun 櫻庭俊