Yanagisawa Keisuke 柳澤渓甫

Researcher Number	40866646
Other IDs
Affiliation (Current)	2025: 東京科学大学, 情報理工学院, 助教
Affiliation (based on the past Project Information) *help	2020 – 2024: 東京工業大学, 情報理工学院, 助教
Review Section/Research Field	Principal Investigator Basic Section 62010:Life, health and medical informatics-related Except Principal Investigator Basic Section 62010:Life, health and medical informatics-related
Keywords	Principal Investigator 標的タンパク質選抜 / 創薬支援計算 / 分子設計 / 環状ペプチド / 共溶媒分子動力学 / マルチタスク深層学習 / 共溶媒分子動力学法 / 網羅的予測 / 畳み込みニューラルネットワーク / マルチタスク学習 / 深層学習 / 隠された結合部位 / リガンド結合部位予測 … More Except Principal Investigator … More ドッキング / SBVS / 化合物データベース / 化合物フラグメント / バーチャルスクリーニング Less

Designing cyclic peptide with target protein selection based on mixed-solvent molecular dynamics simulationPrincipal Investigator
- Principal Investigator
  
  柳澤渓甫
- Project Period (FY)
  2023 – 2026
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 62010:Life, health and medical informatics-related
- Research Institution
  Institute of Science Tokyo
Virtual screening method for large-scale compound databases using commonality in chemical substructures
- Principal Investigator
  
  秋山泰
- Project Period (FY)
  2022 – 2024
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 62010:Life, health and medical informatics-related
- Research Institution
  Institute of Science Tokyo
Comprehensive prediction of cryptic binding sites by multi-task deep learningPrincipal Investigator
- Principal Investigator
  
  Yanagisawa Keisuke
- Project Period (FY)
  2020 – 2022
- Research Category
  
  Grant-in-Aid for Early-Career Scientists
- Review Section
  
  Basic Section 62010:Life, health and medical informatics-related
- Research Institution
  Tokyo Institute of Technology

All 2024 2023 2022 2021 2020

All Journal Article Presentation

[Journal Article] AAp-MSMD: Amino Acid Preference Mapping on Protein-Protein Interaction Surfaces Using Mixed-Solvent Molecular Dynamics2024
- Author(s)
  Genki Kudo, Keisuke Yanagisawa, Ryunosuke Yoshino, and Takatsugu Hirokawa
- Journal Title
  
  Journal of Chemical Information and Modeling
  
  Volume: 63(24) Issue: 24 Pages: 7768-7777
- DOI
  10.1021/acs.jcim.3c01677
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-23K24939, KAKENHI-PROJECT-23K28185
[Journal Article] CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides2023
- Author(s)
  Li Jianan、Yanagisawa Keisuke、Sugita Masatake、Fujie Takuya、Ohue Masahito、Akiyama Yutaka
- Journal Title
  
  Journal of Chemical Information and Modeling
  
  Volume: 63 Issue: 7 Pages: 2240-2250
- DOI
  10.1021/acs.jcim.2c01573
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20H04280, KAKENHI-PROJECT-20K19917, KAKENHI-PROJECT-23K24939, KAKENHI-PROJECT-23KJ0891
[Journal Article] Effective Protein-Ligand Docking Strategy via Fragment Reuse and a Proof-of-Concept Implementation2022
- Author(s)
  Yanagisawa Keisuke、Kubota Rikuto、Yoshikawa Yasushi、Ohue Masahito、Akiyama Yutaka
- Journal Title
  
  ACS Omega
  
  Volume: 7 Issue: 34 Pages: 30265-30274
- DOI
  10.1021/acsomega.2c03470
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20K19917, KAKENHI-PROJECT-23K24939
[Journal Article] Solving Generalized Polyomino Puzzles Using the Ising Model2022
- Author(s)
  Takabatake Kazuki、Yanagisawa Keisuke、Akiyama Yutaka
- Journal Title
  
  Entropy
  
  Volume: 24 Issue: 3 Pages: 354-354
- DOI
  10.3390/e24030354
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20K19917
[Journal Article] Lipid Composition Is Critical for Accurate Membrane Permeability Prediction of Cyclic Peptides by Molecular Dynamics Simulations2022
- Author(s)
  Sugita Masatake、Fujie Takuya、Yanagisawa Keisuke、Ohue Masahito、Akiyama Yutaka
- Journal Title
  
  Journal of Chemical Information and Modeling
  
  Volume: 62 Issue: 18 Pages: 4549-4560
- DOI
  10.1021/acs.jcim.2c00931
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20K19917, KAKENHI-PROJECT-23K24939
[Journal Article] Inverse Mixed-Solvent Molecular Dynamics for Visualization of the Residue Interaction Profile of Molecular Probes2022
- Author(s)
  Yanagisawa Keisuke、Yoshino Ryunosuke、Kudo Genki、Hirokawa Takatsugu
- Journal Title
  
  International Journal of Molecular Sciences
  
  Volume: 23 Issue: 9 Pages: 4749-4749
- DOI
  10.3390/ijms23094749
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20K19917, KAKENHI-PROJECT-23K24939
[Journal Article] EXPRORER: Rational Cosolvent Set Construction Method for Cosolvent Molecular Dynamics Using Large-Scale Computation2021
- Author(s)
  Yanagisawa Keisuke、Moriwaki Yoshitaka、Terada Tohru、Shimizu Kentaro
- Journal Title
  
  Journal of Chemical Information and Modeling
  
  Volume: 61 Issue: 6 Pages: 2744-2753
- DOI
  10.1021/acs.jcim.1c00134
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20K19917
[Journal Article] Virtual Screening Methods with a Protein Tertiary Structure for Drug Discovery2021
- Author(s)
  柳澤渓甫
- Journal Title
  
  JSBi Bioinformatics Review
  
  Volume: 2 Issue: 1 Pages: 76-86
- DOI
  10.11234/jsbibr.2021.9
- NAID
  130008101626
- ISSN
  2435-7022
- Language
  Japanese
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20K19917
[Journal Article] Plasma protein binding prediction focusing on residue-level features and circularity of cyclic peptides by deep learning2021
- Author(s)
  Li Jianan、Yanagisawa Keisuke、Yoshikawa Yasushi、Ohue Masahito、Akiyama Yutaka
- Journal Title
  
  Bioinformatics
  
  Volume: 38 Issue: 4 Pages: 1110-1117
- DOI
  10.1093/bioinformatics/btab726
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20K19917
[Journal Article] Large-Scale Membrane Permeability Prediction of Cyclic Peptides Crossing a Lipid Bilayer Based on Enhanced Sampling Molecular Dynamics Simulations2021
- Author(s)
  Sugita Masatake、Sugiyama Satoshi、Fujie Takuya、Yoshikawa Yasushi、Yanagisawa Keisuke、Ohue Masahito、Akiyama Yutaka
- Journal Title
  
  Journal of Chemical Information and Modeling
  
  Volume: 61 Issue: 7 Pages: 3681-3695
- DOI
  10.1021/acs.jcim.1c00380
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20K19917
[Presentation] フラグメントに基づくバーチャルスクリーニングへの利用などを目指したフラグメント集合の選定2024
- Author(s)
  布部絢子, 柳澤渓甫, 秋山泰
- Organizer
  情報処理学会第77回バイオ情報学研究会 (SIGBIO)
- Data Source
  KAKENHI-PROJECT-23K28185
[Presentation] 分子動力学シミュレーション軌跡データから抽出した位置依存特徴量を活用した環状ペプチドの膜透過性予測2024
- Author(s)
  能祖雄大, 柳澤渓甫, 秋山泰
- Organizer
  情報処理学会第77回バイオ情報学研究会 (SIGBIO)
- Data Source
  KAKENHI-PROJECT-23K28185
[Presentation] CycPeptMP：マルチレベルの分子特徴とデータ拡張による環状ペプチドの膜透過性予測手法の開発2024
- Author(s)
  李佳男, 柳澤渓甫, 秋山泰
- Organizer
  情報処理学会第77回バイオ情報学研究会 (SIGBIO)
- Data Source
  KAKENHI-PROJECT-23K28185
[Presentation] CycPeptMP：マルチレベルの分子特徴とデータ拡張による環状ペプチドの膜透過性予測手法の開発2024
- Author(s)
  李佳男, 柳澤渓甫, 秋山泰
- Organizer
  情報処理学会第77回バイオ情報学研究会 (SIGBIO)
- Data Source
  KAKENHI-PROJECT-23K24939
[Presentation] フラグメントに基づくバーチャルスクリーニングへの利用などを目指したフラグメント集合の選定2024
- Author(s)
  布部絢子, 柳澤渓甫, 秋山泰
- Organizer
  情報処理学会第77回バイオ情報学研究会 (SIGBIO)
- Data Source
  KAKENHI-PROJECT-23K24939
[Presentation] 分子動力学シミュレーション軌跡データから抽出した位置依存特徴量を活用した環状ペプチドの膜透過性予測2024
- Author(s)
  能祖雄大, 柳澤渓甫, 秋山泰
- Organizer
  情報処理学会第77回バイオ情報学研究会 (SIGBIO)
- Data Source
  KAKENHI-PROJECT-23K24939
[Presentation] CycPeptMPDB：包括的な環状ペプチド膜透過率データベースの開発2023
- Author(s)
  李佳男, 柳澤渓甫, 杉田昌岳, 藤江拓哉, 大上雅史, 秋山泰
- Organizer
  情報処理学会第74回バイオ情報学研究会 (SIGBIO)
- Data Source
  KAKENHI-PROJECT-23K28185
[Presentation] CycPeptMPDB：包括的な環状ペプチド膜透過率データベースの開発2023
- Author(s)
  李佳男, 柳澤渓甫, 杉田昌岳, 藤江拓哉, 大上雅史, 秋山泰
- Organizer
  情報処理学会第74回バイオ情報学研究会 (SIGBIO)
- Data Source
  KAKENHI-PROJECT-23K24939
[Presentation] Development of a Protocol for Predicting Membrane Permeability of Cyclic Peptides Based on Molecular Dynamics Simulations2023
- Author(s)
  Masatake Sugita, Takuya Fujie, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama
- Organizer
  第61回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-23K24939
[Presentation] Quantitative Evaluation of Protein-Chemical Substructure Interaction with Inverse Mixed-Solvent Molecular Dynamics Simulation2023
- Author(s)
  Keisuke Yanagisawa, Ryunosuke Yoshino, Genki Kudo, Takatsugu Hirokawa
- Organizer
  第61回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-23K28185
[Presentation] Development of a Protocol for Predicting Membrane Permeability of Cyclic Peptides Based on Molecular Dynamics Simulations2023
- Author(s)
  Masatake Sugita, Takuya Fujie, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama
- Organizer
  第61回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-23K28185
[Presentation] Quantitative Estimation of Protein-Chemical Substructure Interaction with Inverse Mixed-Solvent Molecular Dynamics Simulation2023
- Author(s)
  Keisuke Yanagisawa, Ryunosuke Yoshino, Genki Kudo, Takatsugu Hirokawa
- Organizer
  CBI学会2023年大会
- Data Source
  KAKENHI-PROJECT-23K28185
[Presentation] 薬剤設計のためにはAlphaFoldはまだまだ足りない2023
- Author(s)
  柳澤渓甫
- Organizer
  第12回生命医薬情報学連合大会
- Data Source
  KAKENHI-PROJECT-23K24939
[Presentation] Quantitative Evaluation of Protein-Chemical Substructure Interaction with Inverse Mixed-Solvent Molecular Dynamics Simulation2023
- Author(s)
  Keisuke Yanagisawa, Ryunosuke Yoshino, Genki Kudo, Takatsugu Hirokawa
- Organizer
  第61回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-23K24939
[Presentation] Quantitative Estimation of Protein-Chemical Substructure Interaction with Inverse Mixed-Solvent Molecular Dynamics Simulation2023
- Author(s)
  Keisuke Yanagisawa, Ryunosuke Yoshino, Genki Kudo, Takatsugu Hirokawa
- Organizer
  CBI学会2023年大会
- Data Source
  KAKENHI-PROJECT-23K24939
[Presentation] フラグメント対の相対位置から検索可能な化合物立体配座データベースの構築2023
- Author(s)
  齋藤那哉, 柳澤渓甫, 秋山泰
- Organizer
  情報処理学会第74回バイオ情報学研究会 (SIGBIO)
- Data Source
  KAKENHI-PROJECT-23K28185
[Presentation] フラグメント対の相対位置から検索可能な化合物立体配座データベースの構築2023
- Author(s)
  齋藤那哉, 柳澤渓甫, 秋山泰
- Organizer
  情報処理学会第74回バイオ情報学研究会 (SIGBIO)
- Data Source
  KAKENHI-PROJECT-23K24939
[Presentation] 薬剤設計のためにはAlphaFoldはまだまだ足りない2023
- Author(s)
  柳澤渓甫
- Organizer
  第12回生命医薬情報学連合大会
- Invited
- Data Source
  KAKENHI-PROJECT-23K28185
[Presentation] 分子動力学シミュレーション軌跡データからの環状ペプチドの膜透過性と相関が高い特徴量の抽出2022
- Author(s)
  能祖雄大, 杉田昌岳, 藤江拓哉, 柳澤渓甫, 大上雅史, 秋山泰
- Organizer
  情報処理学会バイオ情報学研究会
- Data Source
  KAKENHI-PROJECT-20K19917
[Presentation] REstretto: An efficient protein-ligand docking tool based on a fragment reuse strategy2022
- Author(s)
  Keisuke Yanagisawa, Rikuto Kubota, Yasushi Yoshikawa, Masahito Ohue, Yutaka Akiyama
- Organizer
  CBI学会2022年大会
- Data Source
  KAKENHI-PROJECT-20K19917
[Presentation] Lipid composition is critical for accurate membrane permeability prediction of cyclic peptides by molecular dynamics simulations2022
- Author(s)
  Masatake Sugita, Takuya Fujie, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama
- Organizer
  CBI学会2022年大会
- Data Source
  KAKENHI-PROJECT-23K24939
[Presentation] Lipid composition is critical for accurate membrane permeability prediction of cyclic peptides by molecular dynamics simulations2022
- Author(s)
  Masatake Sugita, Takuya Fujie, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama
- Organizer
  CBI学会2022年大会
- Data Source
  KAKENHI-PROJECT-20K19917
[Presentation] インバース共溶媒分子動力学法による分子プローブ周辺アミノ酸残基環境の可視化2022
- Author(s)
  柳澤渓甫, 吉野龍ノ介, 工藤玄己, 広川貴次
- Organizer
  第60回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-20K19917
[Presentation] インバース共溶媒分子動力学法による分子プローブ周辺残基環境の可視化2022
- Author(s)
  柳澤渓甫, 吉野龍ノ介, 工藤玄己, 広川貴次
- Organizer
  第22回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-20K19917
[Presentation] インバース共溶媒分子動力学法による分子プローブ周辺アミノ酸残基環境の可視化2022
- Author(s)
  柳澤渓甫, 吉野龍ノ介, 工藤玄己, 広川貴次
- Organizer
  第60回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-23K24939
[Presentation] インバース共溶媒分子動力学法による分子プローブ周辺残基環境の可視化2022
- Author(s)
  柳澤渓甫, 吉野龍ノ介, 工藤玄己, 広川貴次
- Organizer
  第22回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-23K24939
[Presentation] 分子動力学シミュレーション軌跡データからの環状ペプチドの膜透過性と相関が高い特徴量の抽出2022
- Author(s)
  能祖雄大, 杉田昌岳, 藤江拓哉, 柳澤渓甫, 大上雅史, 秋山泰
- Organizer
  情報処理学会バイオ情報学研究会 (SIGBIO)
- Data Source
  KAKENHI-PROJECT-23K24939
[Presentation] Amino Acid Preference Mapping on Protein-Protein Interaction Surface using Mixed-Solvent Molecular Dynamics2022
- Author(s)
  Genki Kudo, Keisuke Yanagisawa, Ryunosuke Yoshino, Takatsugu Hirokawa
- Organizer
  CBI学会2022年大会
- Data Source
  KAKENHI-PROJECT-23K24939
[Presentation] REstretto: An efficient protein-ligand docking tool based on a fragment reuse strategy2022
- Author(s)
  Keisuke Yanagisawa, Rikuto Kubota, Yasushi Yoshikawa, Masahito Ohue, Yutaka Akiyama
- Organizer
  CBI学会2022年大会
- Data Source
  KAKENHI-PROJECT-23K24939
[Presentation] Large-scale membrane permeability prediction of cyclic peptides crossing a lipid bilayer based on enhanced sampling molecular dynamics simulations2021
- Author(s)
  asatake Sugita, Satoshi Sugiyama, Takuya Fujie, Yasushi Yoshikawa, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama
- Organizer
  CBI学会2021年大会
- Data Source
  KAKENHI-PROJECT-20K19917
[Presentation] 分子動力学シミュレーションに基づいた環状ペプチドの膜透過率の大規模予測2021
- Author(s)
  杉田昌岳, 杉山聡, 藤江拓哉, 吉川寧, 柳澤渓甫, 大上雅史, 秋山泰
- Organizer
  第58回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-20K19917
[Presentation] タンパク質表面との結合親和性を考慮した長距離フラグメントリンキング手法の開発2021
- Author(s)
  津嶋佑旗, 柳澤渓甫, 大上雅史, 秋山泰
- Organizer
  第67回情報処理学会バイオ情報学研究会
- Data Source
  KAKENHI-PROJECT-20K19917
[Presentation] フラグメント化された化合物立体構造データベースの構築2021
- Author(s)
  稲垣雅也, 柳澤渓甫, 大上雅史, 秋山泰
- Organizer
  第69回情報処理学会バイオ情報学研究会
- Data Source
  KAKENHI-PROJECT-20K19917
[Presentation] 新たなデータセットによる長距離フラグメントリンキング手法の再評価2021
- Author(s)
  津嶋佑旗, 柳澤渓甫, 大上雅史, 秋山泰
- Organizer
  第69回情報処理学会バイオ情報学研究会
- Data Source
  KAKENHI-PROJECT-20K19917
[Presentation] 共溶媒分子動力学シミュレーションにおける創薬向け共溶媒セットの構築2020
- Author(s)
  柳澤渓甫
- Organizer
  第43回日本分子生物学会年会 (MBSJ2020)
- Data Source
  KAKENHI-PROJECT-20K19917

1. 秋山泰 (30243091)

# of Collaborated Projects: 1 results

# of Collaborated Products: 9 results
2. 吉野龍ノ介 (50817575)

# of Collaborated Projects: 1 results

# of Collaborated Products: 2 results
3. 和久井直樹 (80786038)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
4. 大上雅史

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

Yanagisawa Keisuke 柳澤 渓甫

Research Projects

Research Products

Co-Researchers

Designing cyclic peptide with target protein selection based on mixed-solvent molecular dynamics simulationPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Virtual screening method for large-scale compound databases using commonality in chemical substructures

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Comprehensive prediction of cryptic binding sites by multi-task deep learningPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

[Journal Article] AAp-MSMD: Amino Acid Preference Mapping on Protein-Protein Interaction Surfaces Using Mixed-Solvent Molecular Dynamics2024

Author(s)

Journal Title

DOI

Data Source

[Journal Article] CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides2023

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Effective Protein-Ligand Docking Strategy via Fragment Reuse and a Proof-of-Concept Implementation2022

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Solving Generalized Polyomino Puzzles Using the Ising Model2022

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Lipid Composition Is Critical for Accurate Membrane Permeability Prediction of Cyclic Peptides by Molecular Dynamics Simulations2022

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Inverse Mixed-Solvent Molecular Dynamics for Visualization of the Residue Interaction Profile of Molecular Probes2022

Author(s)

Journal Title

DOI

Data Source

[Journal Article] EXPRORER: Rational Cosolvent Set Construction Method for Cosolvent Molecular Dynamics Using Large-Scale Computation2021

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Virtual Screening Methods with a Protein Tertiary Structure for Drug Discovery2021

Author(s)

Journal Title

DOI

NAID

ISSN

Language

Data Source

[Journal Article] Plasma protein binding prediction focusing on residue-level features and circularity of cyclic peptides by deep learning2021

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Large-Scale Membrane Permeability Prediction of Cyclic Peptides Crossing a Lipid Bilayer Based on Enhanced Sampling Molecular Dynamics Simulations2021

Author(s)

Journal Title

DOI

Data Source

[Presentation] フラグメントに基づくバーチャルスクリーニングへの利用などを目指したフラグメント集合の選定2024

Author(s)

Organizer

Data Source

[Presentation] 分子動力学シミュレーション軌跡データから抽出した位置依存特徴量を活用した環状ペプチドの膜透過性予測2024

Yanagisawa Keisuke 柳澤渓甫