Keisuke Yanagisawa

Assistant Professor, Tokyo Institute of Technology

About me

I’m an assistant professor in Tokyo Institute of Technology. I have proposed several methods with computational, algorithmical, and physicochemical consideration.


Recent news

2024 January-June

  • 2024/06 A poster presentation will be given at the 21st IUPAB and 62nd BSJ joint congress 2024.
    • Keisuke Yanagisawa, Ryunosuke Yoshino, Genki Kudo, Takatsugu Hirokawa. “Quantitative Evaluation of Protein-Compound Substructure Interaction with Inverse Mixed-Solvent Molecular Dynamics Simulation”, 21st IUPAB and 62nd BSJ joint congress 2024, 2024/6/24-28.
  • 2024/06 An oral presentation and a poster presentation will be given at the 24th Annual Meeting of the Protein Science Society of Japan.
    • Keisuke Yanagisawa, Ryunosuke Yoshino, Genki Kudo, Takatsugu Hirokawa. “Quantitative Estimation of Protein-Compound Substructure Interaction with Inverse Mixed-Solvent Molecular Dynamics Simulation”, The 24th Annual Meeting of the Protein Science Society of Japan: [WS-14] バイオインフォマティクスと農芸化学の出会うところ, 2024/06/13.
    • Chie Motono, Keisuke Yanagisawa, Genki Kudo, Takatsugu Hirokawa, Kenichiro Imai. “Cryptic site prediction using mixed-solvent molecular dynamics simulation”, The 24th Annual Meeting of the Protein Science Society of Japan, 2024/06/11-13.
  • 2024/03 Three oral presentations will be given at IPSJ SIG Bioinformatics and Genomics (SIGBIO).
    • Ayako Nunobe, Keisuke Yanagisawa, Yutaka Akiyama. “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”, IPSJ SIG Technical Report, 2022-BIO-77(31): 1-7, 2024/03/08.
    • Yudai Noso, Keisuke Yanagisawa, Yutaka Akiyama. “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”, IPSJ SIG Technical Report, 2022-BIO-77(16): 1-8, 2024/03/07.
    • Jianan Li, Keisuke Yanagisawa, Yutaka Akiyama. “CycPeptMP: Development of Membrane Permeability Prediction of Cyclic Peptides with Multi-Level Molecular Features and Data Augmentation”, IPSJ SIG Technical Report, 2022-BIO-77(15): 1-8, 2024/03/07.

    • 2023 July-December

  • 2023/11 A poster presentation will be given at the 61st Annual Meeting of the Biophysical Society of Japan.
    • Keisuke Yanagisawa, Ryunosuke Yoshino, Genki Kudo, Takatsugu Hirokawa. “Quantitative Evaluation of Protein-Chemical Substructure Interaction with Inverse Mixed-Solvent Molecular Dynamics Simulation”, The 61st Annual Meeting of The Biophysical Society of Japan, 2Pos013, 2023/11/14-16.
  • 2023/10 A poster presentation will be given at Chem-Bio Informatics Society(CBI) Annual Meeting 2023.
    • Keisuke Yanagisawa, Ryunosuke Yoshino, Genki Kudo, Takatsugu Hirokawa. “Quantitative Estimation of Protein-Chemical Substructure Interaction with Inverse Mixed-Solvent Molecular Dynamics Simulation”, Chem-Bio Informatics Society(CBI) Annual Meeting 2023, 2023/10/23-26.
  • 2023/09 An oral presentation will be given at an IIBMP2023 workshop.
    • Keisuke Yanagisawa. “Further and Drastic Improvement of AlphaFold is Needed: Insights from Drug Design”, Informatics in Biology, Medicine, and Pharmacology 2023 (IIBMP2023): [WS-2] バイオインフォマティクスの8の問題, 2023/09/05.

2023 January-June

  • 2023/06 Three oral presentations will be given at IPSJ SIG Bioinformatics and Genomics (SIGBIO).
    • Jianan Li, Keisuke Yanagisawa, Masatake Sugita, Takuya Fujie, Masahito Ohue, Yutaka Akiyama. “CycPeptMPDB：包括的な環状ペプチド膜透過率データベースの開発”, IPSJ SIG Technical Report, 2022-BIO-74(38): 1-8, 2023/07/01.
    • Tomoya Saito, Keisuke Yanagisawa, Yutaka Akiyama. “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”, IPSJ SIG Technical Report, 2022-BIO-74(37): 1-8, 2023/07/01.
    • Ginga Watanabe, Keisuke Yanagisawa, Yutaka Akiyama. “標的RNAの高次構造予測に基づく低活性ASO候補配列の推測”, IPSJ SIG Technical Report, 2022-BIO-74(36): 1-8, 2023/07/01.
  • 2023/03 A paper has been published.
    • Jianan Li, Keisuke Yanagisawa, Masatake Sugita, Takuya Fujie, Masahito Ohue, Yutaka Akiyama. “CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides”, Journal of Chemical Information and Modeling, Journal of Chemical Information and Modeling, 63: 2240-2250, 2023/03. DOI: 10.1021/acs.jcim.2c01573
  • 2023/02 I got a JSPS KAKENHI (grant-in-aid for Scientific Research (B)) with two researchers.
    • “Designing cyclic peptide with target protein selection based on mixed-solvent molecular dynamics simulation”, JSPS KAKENHI (Grant-in-Aid for Scientific Research (B)) 23H03495, PI, 18 590 000 yen, 2023/04-2027/03.

2022 July-December

  • 2022/10 two oral presentations and a poster presentation had been given at Chem-Bio Informatics Society(CBI) Annual Meeting 2022.
    • Keisuke Yanagisawa, Rikuto Kubota, Yasushi Yoshikawa, Masahito Ohue, Yutaka Akiyama. “REstretto: An efficient protein-ligand docking tool based on a fragment reuse strategy”, Chem-Bio Informatics Society(CBI) Annual Meeting 2022, O2-1, 2022/10/25.
    • Masatake Sugita, Takuya Fujie, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama. “Lipid composition is critical for accurate membrane permeability prediction of cyclic peptides by molecular dynamics simulations”, Chem-Bio Informatics Society(CBI) Annual Meeting 2022, O3-2, 2022/10/25.
    • Genki Kudo, Keisuke Yanagisawa, Ryunosuke Yoshino, Takatsugu Hirokawa. “Amino Acid Preference Mapping on Protein-Protein Interaction Surface using Mixed-Solvent Molecular Dynamics”, Chem-Bio Informatics Society(CBI) Annual Meeting 2022, P02-04, 2022/10/25-27.
  • 2022/09 A poster presentation will be given at the 60th Annual Meeting of the Biophysical Society of Japan.
    • Keisuke Yanagisawa, Ryunosuke Yoshino, Genki Kudo, Takatsugu Hirokawa. “Inverse Mixed-Solvent Molecular Dynamics for Visualization of Amino Acid Residue Interaction Profile of Molecular Probes”, The 60th Annual Meeting of The Biophysical Society of Japan, 1Pos031, 2022/09/28.
  • 2022/09 A paper has been published.
    • Masatake Sugita, Takuya Fujie, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama. “Lipid composition is critical for accurate membrane permeability prediction of cyclic peptides by molecular dynamics simulations”, Journal of Chemical Information and Modeling, 62: 4549-4560, 2022/09. DOI: 10.1021/acs.jcim.2c00931
  • 2022/08 A paper has been published.
    • Keisuke Yanagisawa, Rikuto Kubota, Yasushi Yoshikawa, Masahito Ohue, Yutaka Akiyama. “Effective protein-ligand docking strategy via fragment reuse and a proof-of-concept implementation”, ACS Omega, 7: 30265-30274, 2022/08. DOI: 10.1021/acsomega.2c03470

2022 January-June

  • 2022/06 An oral presentation will be given at IPSJ SIG Bioinformatics and Genomics (SIGBIO).
    • Yudai Noso, Masatake Sugita, Takuya Fujie, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama. “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”, IPSJ SIG Technical Report, 2022-BIO-70(51): 1-8, 2022/06/29.
  • 2022/06 An oral presentation will be given at the 22nd Annual Meeting of the Protein Science Society of Japan (PSSJ2022).
    • Keisuke Yanagisawa, Ryunosuke Yoshino, Genki Kudo, Takatsugu Hirokawa. “Inverse Mixed-Solvent Molecular Dynamics for Visualization of Residue Interaction Profile of Molecular Probes”, The 22nd Annual Meeting of the Protein Science Society of Japan, O7-12, 2022/06/07.
  • 2022/06 I got a grant for young researcher.
    • “Recognition of protein surface where suitable for ligand binding with Inverse-MSMD simulations”, Grant for young researcher, School of Computing, Tokyo Institute of Technology, PI, 500 000 yen, 2022/06-2023/03.
  • 2022/04 A paper has been published.
    • Keisuke Yanagisawa, Ryunosuke Yoshino, Genki Kudo, Takatsugu Hirokawa. “Inverse Mixed-Solvent Molecular Dynamics for Visualization of the Residue Interaction Profile of Molecular Probes”, International Journal of Molecular Sciences, 23: 4749, 2022/04. DOI: 10.3390/ijms23094749
  • 2022/03 Four oral presentation will be given at IPSJ SIG Bioinformatics and Genomics (SIGBIO).
    • Yuki Tsushima, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama. “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”, IPSJ SIG Technical Report, 2021-BIO-69(16): 1-8, 2022/03/11.
    • Masaya Inagaki, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama. “Database of Drug Candidates Represented by 3D Positional Relationships between Fragments”, IPSJ SIG Technical Report, 2021-BIO-69(15): 1-8, 2022/03/11.
    • Mahiro Yamazaki, Kazuki Izawa, Ryo Hirata, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama. “Development of a Genome-wide Fast Short Nucleotide Sequence Search Method Considering Binding Energy”, IPSJ SIG Technical Report, 2021-BIO-69(8): 1-8, 2022/03/10.
    • Shu Tamano, Kazuki Izawa, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama. “Proposal of Evaluation Off-target Effects Method in Gapmer ASO”, IPSJ SIG Technical Report, 2021-BIO-69(7): 1-7, 2022/03/10.
  • 2022/02 A paper has been published.
    • Kazuki Takabatake, Keisuke Yanagisawa, Yutaka Akiyama. “Solving Generalized Polyomino Puzzles Using the Ising Model”, Entropy, 24: 354, 2022/02. DOI: 10.3390/e24030354

News archive

News archive


Tools

EXPRORER (2021)

EXPRORER

Rational cosolvent set construction with cosolvent MD simulation results

https://github.com/keisuke-yanagisawa/exprorer

Spresso (2017)

Spresso

An ultrafast pre-screening method based on compound decomposition

https://www.bi.cs.titech.ac.jp/spresso