Akiyama Yutaka 秋山泰

… Alternative Names

AKIYAMA Yutaka 秋山泰

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Researcher Number	30243091
Other IDs	https://orcid.org/0000-0003-2863-8703
Affiliation (Current)	2024: 東京科学大学, 情報理工学院, 教授
Affiliation (based on the past Project Information) *help	2016 – 2024: 東京工業大学, 情報理工学院, 教授 2012 – 2015: 東京工業大学, 情報理工学(系)研究科, 教授 2010: 東京工業大学, 情報理工学研究科, 教授 2007 – 2010: Tokyo Institute of Technology, 大学院・情報理工学研究科, 教授 2008: 東京工業大学, 大学院情報理工学研究科, 教授 … More 2007 – 2008: 国立大学法人東京工業大学, 大学院・情報理工学研究科, 教授 2006: 東京工業大学, 大学院情報理工学研究科, 教授 2006: 独立行政法人産業技術研究所, 生命情報科学研究センター, 研究センター長 2005: 独立行政法人産業技術総合研究所, 生命情報科学研究センター, 研究センター長 Less
Review Section/Research Field	Principal Investigator Bioinformatics/Life informatics / Basic Section 62010:Life, health and medical informatics-related / Life / Health / Medical informatics Except Principal Investigator Basic Section 58020:Hygiene and public health-related: including laboratory approach / Basic Section 52050:Embryonic medicine and pediatrics-related / Life / Health / Medical informatics / Software / Science and Engineering
Keywords	Principal Investigator 生体生命情報学 / 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 / 深層学習 / 機械学習 / 分子動力学法 / 血漿タンパク質結合率 … More / 膜透過性 / 中分子創薬 / 環状ペプチド / 生命生体情報学 / 分子シミュレーション / ハイパフォーマンス・コンピューティング / 薬学 / アルゴリズム / バイオインフォマティクス / 高性能計算 / 蛋白質 / コンピュータシミュレーション … More Except Principal Investigator バイオインフォマティクス / アレルギー / ダニ / 住環境 / ダニアレルゲン / 真菌 / ハウスダスト / 酵母 / カビ / ヒョウヒダニ / フェロトーシス / 細胞死 / 酸化ストレス / ミトコンドリア / 非アルコール性脂肪性肝疾患 / アルツハイマー病 / パーキンソン病 / ミトコンドリア病 / アポモルフィン / 抗寄生原虫治療薬 / in vitroアッセイ / in silico創薬 / ハイパフォーマンス・コンピューティング / 量子化学計算 / 分子シミュレーション / スーパーコンピューティング / コンピュータシミュレーション / 創薬 / 機械学習 / SDGs / 顧みられない熱帯病 / スーパーコンピュータ / IT創薬 / ケモインフォマティクス / スマート創薬 / 並列分散システム / オペレーティングシステム / 分散共有メモリシステム / 大規模メモリ空間 / OS / クラスタ / 大規模メモリ / 分散ページ / PCクラスタ / リモートスワップ / I細胞解析 / RNA検出 / RNA回収 / デジタル精密解析 / RNA 検出 / RNA 回収 / 磁気ビーズ / パイロシークエンス / デジタル精密計測 / 1細胞解析 / ライフサーベイヤ Less

Virtual screening method for large-scale compound databases using commonality in chemical substructuresPrincipal Investigator
- 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
  Tokyo Institute of Technology
Research on the relevance between fungal growth and mite population
- Principal Investigator
  
  渡辺麻衣子
- Project Period (FY)
  2021 – 2023
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Review Section
  
  Basic Section 58020:Hygiene and public health-related: including laboratory approach
- Research Institution
  National Institute of Health Sciences
Elucidation of the mechanism of mitochondrial disease cell death inhibition and drug discovery
- Principal Investigator
  
  Osaka Hitoshi
- Project Period (FY)
  2020 – 2022
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 52050:Embryonic medicine and pediatrics-related
- Research Institution
  Jichi Medical University
Development of computational methods for supporting druggable cyclic peptide designPrincipal Investigator
- Principal Investigator
  
  Akiyama Yutaka
- Project Period (FY)
  2017 – 2019
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Research Field
  
  Life / Health / Medical informatics
- Research Institution
  Tokyo Institute of Technology
In silico, in vitro, X-ray crystallography, and integrated strategies for discovering spermidine synthase inhibitors for Chagas disease
- Principal Investigator
  
  SEKIJIMA MASAKAZU
- Project Period (FY)
  2015 – 2018
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Research Field
  
  Life / Health / Medical informatics
- Research Institution
  Tokyo Institute of Technology
Computational drug discovery techniques with systematic target identification and high-performance molecular simulationPrincipal Investigator
- Principal Investigator
  
  Akiyama Yutaka
- Project Period (FY)
  2012 – 2016
- Research Category
  
  Grant-in-Aid for Scientific Research (A)
- Research Field
  
  Bioinformatics/Life informatics
- Research Institution
  Tokyo Institute of Technology
An exhaustive all-to-all protein-protein interaction prediction algorithm based on 3-D shape complimentarity and its statistical distribution on protein surface.Principal Investigator
- Principal Investigator
  
  AKIYAMA Yutaka
- Project Period (FY)
  2007 – 2010
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Research Field
  
  Bioinformatics/Life informatics
- Research Institution
  Tokyo Institute of Technology
Large Virtual Memory Space Supporting System on Next Generation PC Clusters
- Principal Investigator
  
  ISHIKAWA Yutaka
- Project Period (FY)
  2006 – 2008
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Research Field
  
  Software
- Research Institution
  The University of Tokyo
The development of accurate quantitative and digital tools for Lifesurveyor
- Principal Investigator
  
  KAMBARA Hideki
- Project Period (FY)
  2005 – 2008
- Research Category
  
  Grant-in-Aid for Scientific Research on Priority Areas
- Review Section
  
  Science and Engineering
- Research Institution
  Tokyo University of Agriculture and Technology

[Book] 一細胞定量解析の最前線-ライフサーベイヤ構築に向けて-(シーエムシー出版)2006
- Author(s)
  秋山泰
- Total Pages
  11
- Publisher
  細胞丸ごとRNA解析に必要となる情報処理の流れ(第5章6節pp.254-364)
- Data Source
  KAKENHI-PROJECT-17066002
[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
[Journal Article] Amide-to-ester substitution as a stable alternative to N-methylation for increasing membrane permeability in cyclic peptides.2023
- Author(s)
  Hosono Y, Uchida S, Shinkai M, Townsend CE, Kelly CN, Naylor MR, Lee HW, Kanamitsu K, Ishii M, Ueki R, Ueda T, Takeuchi K, Sugita M, Akiyama Y, Lokey SR, Morimoto J, Sando S.
- Journal Title
  
  Nat. Commun.
  
  Volume: 14 Issue: 1 Pages: 1416-1416
- DOI
  10.1038/s41467-023-36978-z
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-21H05509, KAKENHI-PROJECT-20H03375, KAKENHI-PROJECT-23K24939
[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] 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] Development of computational pipeline software for genome/exome analysis on the K computer2020
- Author(s)
  Aoyama Kento, Kakuta Masanori, Matsuzaki Yuri, Ishida Takashi, Ohue Masahito, Akiyama Yutaka
- Journal Title
  
  Supercomputing Frontiers and Innovations
  
  Volume: accepted
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17H01814
[Journal Article] Multidomain protein structure prediction using information about residues interacting on multimeric protein interfaces2020
- Author(s)
  Matsuno Shumpei, Ohue Masahito, Akiyama Yutaka
- Journal Title
  
  Biophysics and Physicobiology
  
  Volume: 17 Issue: 0 Pages: 2-13
- DOI
  10.2142/biophysico.BSJ-2019050
- NAID
  130007795865
- ISSN
  2189-4779
- Language
  English
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-17H01814, KAKENHI-PROJECT-18K18149
[Journal Article] NRLMFβ: Beta-distribution-rescored neighborhood regularized logistic matrix factorization for improving the performance of drug?target interaction prediction2019
- Author(s)
  Ban Tomohiro、Ohue Masahito、Akiyama Yutaka
- Journal Title
  
  Biochemistry and Biophysics Reports
  
  Volume: 18 Pages: 100615-100615
- DOI
  10.1016/j.bbrep.2019.01.008
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-18K18149, KAKENHI-PROJECT-15H02776, KAKENHI-PROJECT-17H01814
[Journal Article] Learning-to-rank technique based on ignoring meaningless ranking orders between compounds2019
- Author(s)
  Ohue Masahito, Suzuki Shogo D., Akiyama Yutaka
- Journal Title
  
  Journal of Molecular Graphics and Modelling
  
  Volume: 92 Pages: 192-200
- DOI
  10.1016/j.jmgm.2019.07.009
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-17H01814, KAKENHI-PROJECT-18K18149
[Journal Article] Multiple grid arrangement improves ligand docking with unknown binding sites: Application to the inverse docking problem2018
- Author(s)
  Tomohiro Ban, Masahito Ohue, and Yutaka Akiyama
- Journal Title
  
  Computational Biology and Chemistry
  
  Volume: 73 Pages: 139-146
- DOI
  10.1016/j.compbiolchem.2018.02.008
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15J11261, KAKENHI-PROJECT-15K16081, KAKENHI-PROJECT-17H01814
[Journal Article] Optimization of memory use of fragment extension-based protein-ligand docking with an original fast minimum cost flow algorithm2018
- Author(s)
  Yanagisawa Keisuke、Komine Shunta、Kubota Rikuto、Ohue Masahito、Akiyama Yutaka
- Journal Title
  
  Computational Biology and Chemistry
  
  Volume: 印刷中 Pages: 399-406
- DOI
  10.1016/j.compbiolchem.2018.03.013
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-15K16081, KAKENHI-PROJECT-15H02776, KAKENHI-PROJECT-17H01814, KAKENHI-PROJECT-17J06897
[Journal Article] In Silico Prediction of Major Clearance Pathways of Drugs among 9 Routes with Two-Step Support Vector Machines2018
- Author(s)
  Wakayama Naomi、Toshimoto Kota、Maeda Kazuya、Hotta Shun、Ishida Takashi、Akiyama Yutaka、Sugiyama Yuichi
- Journal Title
  
  Pharmaceutical Research
  
  Volume: 35 Issue: 10 Pages: 1-21
- DOI
  10.1007/s11095-018-2479-1
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15H02776, KAKENHI-PROJECT-17H01814
[Journal Article] MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions.2018
- Author(s)
  Takanori Hayashi, Yuri Matsuzaki, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama
- Journal Title
  
  BMC Bioinformatics
  
  Volume: 19 Issue: S4 Pages: 62-72
- DOI
  10.1186/s12859-018-2073-x
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16K00388, KAKENHI-PROJECT-18K18149, KAKENHI-PROJECT-17H01814, KAKENHI-PROJECT-17J06897
[Journal Article] Computational prediction of plasma protein binding of cyclic peptides from small molecule experimental data using sparse modeling techniques2018
- Author(s)
  Tajimi Takashi、Wakui Naoki、Yanagisawa Keisuke、Yoshikawa Yasushi、Ohue Masahito、Akiyama Yutaka
- Journal Title
  
  BMC Bioinformatics
  
  Volume: 19 Issue: S19 Pages: 527-527
- DOI
  10.1186/s12859-018-2529-z
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-18K18149, KAKENHI-PROJECT-17H01814, KAKENHI-PROJECT-17J06897
[Journal Article] QEX: target-specific druglikeness filter enhances ligand-based virtual screening2018
- Author(s)
  Mochizuki Masahiro、Suzuki Shogo D.、Yanagisawa Keisuke、Ohue Masahito、Akiyama Yutaka
- Journal Title
  
  Molecular Diversity
  
  Volume: 23 Issue: 1 Pages: 11-18
- DOI
  10.1007/s11030-018-9842-3
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-15H02776, KAKENHI-PROJECT-17H01814, KAKENHI-PROJECT-17J06897
[Journal Article] An iterative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes2017
- Author(s)
  Shuntaro Chiba, 他30名（George Chikenji は16番目の著者）
- Journal Title
  
  Scientific Reports
  
  Volume: 7 Issue: 1 Pages: 1-13
- DOI
  10.1038/s41598-017-10275-4
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16K07315, KAKENHI-PROJECT-15H02776, KAKENHI-PROJECT-17H01814, KAKENHI-PROJECT-16J09021, KAKENHI-PROJECT-17J06897
[Journal Article] In silico, in vitro, X-ray crystallography, and integrated strategies for discovering spermidine synthase inhibitors for Chagas disease2017
- Author(s)
  Yoshino Ryunosuke、Yasuo Nobuaki、Hagiwara Yohsuke、Ishida Takashi、Inaoka Daniel Ken、Amano Yasushi、Tateishi Yukihiro、Ohno Kazuki、Namatame Ichiji、Niimi Tatsuya、Orita Masaya、Kita Kiyoshi、Akiyama Yutaka、Sekijima Masakazu
- Journal Title
  
  Scientific Reports
  
  Volume: 7 Issue: 1 Pages: 1-9
- DOI
  10.1038/s41598-017-06411-9
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-15H02776, KAKENHI-PROJECT-17H01814, KAKENHI-PROJECT-16J09021, KAKENHI-PROJECT-15K16082, KAKENHI-PROJECT-16K19114
[Journal Article] Identification of type I and type II inhibitors of c-Yes kinase using in silico and experimental techniques2017
- Author(s)
  Ramakrishnan Chandrasekaran、Mary Thangakani Anthony、Velmurugan Devadasan、Anantha Krishnan Dhanabalan、Sekijima Masakazu、Akiyama Yutaka、Gromiha M. Michael
- Journal Title
  
  Journal of Biomolecular Structure and Dynamics
  
  Volume: 36 Issue: 6 Pages: 1566-1576
- DOI
  10.1080/07391102.2017.1329098
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15H02776, KAKENHI-PROJECT-17H01814
[Journal Article] Link Mining for Kernel-Based Compound-Protein Interaction Predictions Using a Chemogenomics Approach2017
- Author(s)
  Ohue Masahito、Yamazaki Takuro、Ban Tomohiro、Akiyama Yutaka
- Journal Title
  
  In Proceedings of the Thirteenth International Conference On Intelligent Computing (ICIC2017) (Lecture Notes in Computer Science)
  
  Volume: － Pages: 549-558
- DOI
  10.1007/978-3-319-63312-1_48
- ISBN
  9783319633114, 9783319633121
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15H02776, KAKENHI-PROJECT-15K16081
[Journal Article] Learning-to-rank based compound virtual screening by using pairwise kernel with multiple heterogeneous experimental data2017
- Author(s)
  Suzuki SD, Ohue M, Akiyama Y
- Journal Title
  
  Proceedings of The 22nd International Symposium on Artificial Life and Robotics (AROB 2017)
  
  Volume: ー Pages: 114-119
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-24240044
[Journal Article] A Massively Parallel Sequence Similarity Search for Metagenomic Sequencing Data2017
- Author(s)
  Kakuta Masanori、Suzuki Shuji、Izawa Kazuki、Ishida Takashi、Akiyama Yutaka
- Journal Title
  
  International Journal of Molecular Sciences
  
  Volume: 18 Issue: 10 Pages: 2124-2124
- DOI
  10.3390/ijms18102124
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-17H01814
[Journal Article] PKRank: a novel learning-to-rank method for ligand-based virtual screening using pairwise kernel and RankSVM2017
- Author(s)
  Suzuki Shogo D.、Ohue Masahito、Akiyama Yutaka
- Journal Title
  
  Artificial Life and Robotics
  
  Volume: － Issue: 2 Pages: 205-212
- DOI
  10.1007/s10015-017-0416-8
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-15H02776, KAKENHI-PROJECT-15K16081, KAKENHI-PROJECT-17H01814
[Journal Article] Efficient hyperparameter optimization by using Bayesian optimization for drug-target interaction prediction2017
- Author(s)
  Ban Tomohiro、Ohue Masahito、Akiyama Yutaka
- Journal Title
  
  In Proceedings of the 7th IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS 2017)
  
  Volume: － Pages: 1-8
- DOI
  10.1109/iccabs.2017.8114299
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-15H02776, KAKENHI-PROJECT-15K16081
[Journal Article] Learning-to-rank based compound virtual screening by using pairwise kernel with multiple heterogeneous experimental data2017
- Author(s)
  Shogo D. Suzuki, Masahito Ohue, Takashi Ishida, Yutaka Akiyama
- Journal Title
  
  Proceedings of The 22nd International Symposium on Artificial Life and Robotics (AROB 2017)
  
  Volume: - Pages: 114-119
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15H02776
[Journal Article] Spresso: An ultrafast compound pre-screening method based on compound decomposition2017
- Author(s)
  Keisuke Yanagisawa, Shunta Komine, Shogo D. Suzuki, Masahito Ohue, Takashi Ishida, Yutaka Akiyama
- Journal Title
  
  Bioinformatics
  
  Volume: 印刷中 Issue: 23 Pages: 3836-3843
- DOI
  10.1093/bioinformatics/btx178
- Peer Reviewed / Acknowledgement Compliant / Open Access
- Data Source
  KAKENHI-PROJECT-24240044, KAKENHI-PROJECT-15H02776, KAKENHI-PROJECT-15K16081, KAKENHI-PROJECT-15K16082, KAKENHI-PROJECT-17H01814, KAKENHI-PROJECT-17J06897
[Journal Article] GHOSTX: A Fast Sequence Homology Search Tool for Functional Annotation of Metagenomic Data2017
- Author(s)
  Suzuki Shuji、Ishida Takashi、Ohue Masahito、Kakuta Masanori、Akiyama Yutaka
- Journal Title
  
  Protein Function Prediction
  
  Volume: volume 1611 Pages: 15-25
- DOI
  10.1007/978-1-4939-7015-5_2
- ISBN
  9781493970131, 9781493970155
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17H01814
[Journal Article] Development of a Support Vector Machine-Based System to Predict　Whether a Compound Is a Substrate of a Given Drug Transporter　Using Its Chemical Structure2016
- Author(s)
  Atsushi Ose, Kota Toshimoto, Kazushi Ikeda, Kazuya Maeda, Shuya Yoshida, Fumiyoshi Yamashita, Mitsuru Hashida, Takashi Ishida, Yutaka Akiyama and Yuichi Sugiyama
- Journal Title
  
  Journal of Pharmaceuticl Sciences
  
  Volume: 印刷中
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15H02776
[Journal Article] スーパーコンピュータ「京」上でのエクソーム解析パイプラインの開発2016
- Author(s)
  青山健人、角田将典、松崎由理、石田貴士、秋山泰
- Journal Title
  
  情報処理学会論文誌コンピューティングシステム
  
  Volume: in press
- NAID
  170000148059
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-24240044
[Journal Article] Rigid-Docking Approaches to Explore Protein-Protein Interaction Space2016
- Author(s)
  Yuri Matsuzaki, Nobuyuki Uchikoga Masahito Ohue, Yutaka Akiyama
- Journal Title
  
  Advances in Biochemical Engineering/Biotechnology
  
  Volume: ー Pages: 1-23
- DOI
  10.1007/10_2016_41
- ISBN
  9783319564593, 9783319564609
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-24240044, KAKENHI-PROJECT-15K00407, KAKENHI-PROJECT-16K00388, KAKENHI-PROJECT-15K16081, KAKENHI-PROJECT-15H02776, KAKENHI-PROJECT-17H01814
[Journal Article] Development of a Support Vector Machine-Based System to Predict Whether a Compound Is a Substrate of a Given Drug Transporter Using Its Chemical Structure2016
- Author(s)
  Atsushi Ose, Kota Toshimoto*, Kazushi Ikeda, Kazuya Maeda, Shuya Yoshida, Fumiyoshi Yamashita, Mitsuru Hashida, Takashi Ishida, Yutaka Akiyama and Yuichi Sugiyama
- Journal Title
  
  Journal of Pharmaceuticl Sciences
  
  Volume: accepted
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-24240044
[Journal Article] Specificity of broad protein interaction surfaces for proteins with multiple binding partners2016
- Author(s)
  Nobuyuki Uchikoga, Yuri Matsuzaki, Masahito Ohue, Yutaka Akiyama
- Journal Title
  
  Biophysics and Physicobiology
  
  Volume: 13 Issue: 0 Pages: 105-115
- DOI
  10.2142/biophysico.13.0_105
- NAID
  130005165366
- ISSN
  2189-4779
- Language
  English
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-24240044, KAKENHI-PROJECT-15H02776, KAKENHI-PROJECT-15K00407, KAKENHI-PROJECT-16K00388, KAKENHI-PROJECT-15K16081
[Journal Article] スーパーコンピュータ「京」上でのエクソーム解析パイプラインの開発2016
- Author(s)
  青山健人、角田将典、松崎由理、石田貴士、秋山泰
- Journal Title
  
  情報処理学会論文誌コンピューティングシステム
  
  Volume: 印刷中
- NAID
  170000148059
- Data Source
  KAKENHI-PROJECT-15H02776
[Journal Article] Drug Clearance Pathway Prediction Based on Semi-supervised Learning2015
- Author(s)
  Keisuke Yanagisawa, Takashi Ishida, Yutaka Akiyama
- Journal Title
  
  IPSJ Transactions on Bioinformatics
  
  Volume: 8 Issue: 0 Pages: 21-27
- DOI
  10.2197/ipsjtbio.8.21
- NAID
  130005094265
- ISSN
  1882-6679
- Language
  English
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-15H02776
[Journal Article] Drug Clearance Pathway Prediction Based on Semi-supervised Learning2015
- Author(s)
  Keisuke Yanagisawa, Takashi Ishida, Yutaka Akiyama
- Journal Title
  
  IPSJ Transactions on Bioinformatics
  
  Volume: 8 Pages: 21-27
- NAID
  130005094265
- Data Source
  KAKENHI-PROJECT-24240044
[Journal Article] Protein-Protein Docking on Hardware Accelerators: Comparison of GPU and MIC Architectures2015
- Author(s)
  Takehiro Shimoda, Shuji Suzuki, Masahito Ohue, Takashi Ishida, Yutaka Akiyama
- Journal Title
  
  BMC Systems Bilogy
  
  Volume: 9 Issue: S1 Pages: 1-10
- DOI
  10.1186/1752-0509-9-s1-s6
- Peer Reviewed / Acknowledgement Compliant / Open Access
- Data Source
  KAKENHI-PROJECT-14J30002, KAKENHI-PROJECT-24240044
[Journal Article] Faster sequence homology searches by clustering subsequences2015
- Author(s)
  Shuji Suzuki, Masanori Kakuta, Takashi Ishida, Yutaka Akiyama
- Journal Title
  
  Bioinformatics
  
  Volume: 31 Issue: 8 Pages: 1183-1190
- DOI
  10.1093/bioinformatics/btu780
- Description
  【掲載確定】印刷中
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-12J08766, KAKENHI-PROJECT-24240044, KAKENHI-PROJECT-15H02776
[Journal Article] Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target2015
- Author(s)
  Chiba S, Akiyama Y, Sekijima M.
- Journal Title
  
  Scientific Reports
  
  Volume: 5 Issue: 1 Pages: 1-13
- DOI
  10.1038/srep17209
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-24240044, KAKENHI-PROJECT-15H02776, KAKENHI-PROJECT-15J11261, KAKENHI-PROJECT-25430186, KAKENHI-PROJECT-26730152, KAKENHI-PUBLICLY-26120528
[Journal Article] Drug clearance pathway prediction based on semi-supervised learning2015
- Author(s)
  K. Yanagisawa, T. Ishida, and Y. Akiyama
- Journal Title
  
  IPSJ Transaction on Bioinformatics
  
  Volume: 未定
- NAID
  130005094265
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-24240044
[Journal Article] Extreme Big Data (EBD): Next Generation Big Data Infrastructure Technologies Towards Yottabyte/Year2014
- Author(s)
  Matsuoka S, Sato H, Tatebe O, Koibuchi M, Fujiwara I, Suzuki S, Kakuta M, Ishida T, Akiyama Y, Suzumura T, Ueno K, Kanezashi H, Miyoshi T.
- Journal Title
  
  Supercomputing Frontiers and Innovations,
  
  Volume: 1(2) Issue: 2 Pages: 89-107
- DOI
  10.14529/jsfi140206
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-24240044
[Journal Article] MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers2014
- Author(s)
  Masahito Ohue, Takehiro Shimoda, Shuji Suzuki, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama
- Journal Title
  
  Bioinformatics
  
  Volume: 30 Issue: 22 Pages: 3281-3283
- DOI
  10.1093/bioinformatics/btu532
- Peer Reviewed / Acknowledgement Compliant / Open Access
- Data Source
  KAKENHI-PROJECT-14J30002, KAKENHI-PROJECT-24240044
[Journal Article] Improvement of a confomational search on protein-ligand docking based on optimal arrangement of multiple small search grids2014
- Author(s)
  Tomohiro Ban, Takashi Ishida, Yutaka Akiyama
- Journal Title
  
  Proc. The 2014 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA'14)
  
  Volume: P2014(PDP4199) Pages: 1-6
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-24240044
[Journal Article] An empirical model for gas phase acidity and basicity estimation2014
- Author(s)
  You H , Kim GE , Na CH , Lee S , Lee CJ , Cho KH , Akiyama Y , Ishida T , No KT.
- Journal Title
  
  SAR and QSAR in Environmental Research
  
  Volume: Volume 25, Issue 2 Issue: 2 Pages: 91-115
- DOI
  10.1080/1062936x.2013.864997
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-24240044
[Journal Article] In silico prediction of major drug clearance pathways by support vector machines with feature-selected descriptors2014
- Author(s)
  Toshimoto K, Wakayama N, Kusama M, Maeda K, Sugiyama Y, Akiyama Y.
- Journal Title
  
  Drug Metabolism and Disposition
  
  Volume: 42(11) Issue: 11 Pages: 1811-1819
- DOI
  10.1124/dmd.114.057893
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-24240044
[Journal Article] MEGADOCK: An all-to-all protein-protein interaction prediction system using tertiary structure data2014
- Author(s)
  Masahito Ohue, Yuri Matsuzaki, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama:
- Journal Title
  
  Protein and Peptide Letters
  
  Volume: 21 Issue: 8 Pages: 766-778
- DOI
  10.2174/09298665113209990050
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-14J30002, KAKENHI-PROJECT-24240044
[Journal Article] Protein-protein interaction network prediction by using rigid-body docking tools: application to bacterial chemotaxis2014
- Author(s)
  Yuri Matsuzaki, Masahito Ohue, Nobuyuki Uchikoga, Yutaka Akiyama
- Journal Title
  
  Protein and Peptide Letters
  
  Volume: 21 Issue: 8 Pages: 790-798
- DOI
  10.2174/09298665113209990066
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-14J30002, KAKENHI-PROJECT-24240044
[Journal Article] Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints2013
- Author(s)
  Nobuyuki Uchikoga, Yuri Matsuzaki, Masahito Ohue, Takatsugu Hirokawa, Yutaka Akiyama
- Journal Title
  
  PLOS ONE
  
  Volume: 8 Issue: 7 Pages: e69365-e69365
- DOI
  10.1371/journal.pone.0069365
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-11J08750, KAKENHI-PROJECT-24240044
[Journal Article] MEGADOCK: An all-to-all protein-protein interaction prediction system using tertiary structure data2013
- Author(s)
  Ohue M, Matsuzaki Y, Uchikoga N, Ishida T, Akiyama Y
- Journal Title
  
  Protein and Peptide Letters
  
  Volume: Vol. 20
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-24240044
[Journal Article] MEGADOCK 3.0 : A high-performance protein-protein interaction prediction software using hybrid parallel computing for petascale supercomputing emvironmnts2013
- Author(s)
  Yuri Matsuzaki, Nobuyuki Uchikoga, Masahito Ohue, Takehiro Shimoda, Tbshiyuki Sato, Takashi Ishida, Yutaka Akiyama
- Journal Title
  
  Source Code for Biology and Medicine
  
  Volume: 8 Issue: 1 Pages: 18-18
- DOI
  10.1186/1751-0473-8-18
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-11J08750, KAKENHI-PROJECT-24240044
[Journal Article] Highly Precise Protein-Protein Interaction Prediction Based on Consens us Between Template-Based and de Novo Docking Methods2013
- Author(s)
  Masahito Ohue, Yuri Matsuzaki, Takehiro Shimoda, Takashi Ishida, Yutaka Akiyama
- Journal Title
  
  BMC Proceedings
  
  Volume: 7 Issue: S7
- DOI
  10.1186/1753-6561-7-s7-s6
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-11J08750, KAKENHI-PROJECT-24240044
[Journal Article] Protein-protein interaction network prediction by using rigid-body docking tools: application to bacterial chemotaxis2013
- Author(s)
  Matsuzaki Y, Ohue M, Uchikoga N, Akiyama Y
- Journal Title
  
  Protein and Peptide Letters
  
  Volume: Vol. 20
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-24240044
[Journal Article] Accelerating quantum chemistry calculations with graphical processing units - toward in high-density (HD) silico drug discovery2013
- Author(s)
  Hagiwara Y , Ohno K , Orita M , Koga R , Endo T , Akiyama Y , Sekijima M.
- Journal Title
  
  Curr Comput Aided Drug Des. 2013
  
  Volume: Vol. 9, No. 3, Pages: 396-401
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-24240044
[Journal Article] Docking-calculation-based Method for Predicting Protein-RNA Interactions2011
- Author(s)
  Masahito Ohue, Yuri Matsuzaki, Yutaka Akiyama
- Journal Title
  
  Genome Informatics
  
  Volume: 25
- NAID
  130004567841
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19300102
[Journal Article] In silico classification of major clearance pathways of drugs with their physicochemical parameters2010
- Author(s)
  Makiko Kusama, Kouta Toshimoto, Kazuya Maeda, Yuka Hirai, Satoki Imai, Koji Chiba, Yutaka Akiyama, Yuichi Sugiyama
- Journal Title
  
  Drug Metabolism and Disposition 28(8)
  
  Pages: 1362-1370
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19300102
[Journal Article] 立体構造情報からの網羅的タンパク質間相互作用予測とそのシステム生物学への応用2010
- Author(s)
  大上雅史, 松崎由理, 松崎祐介, 佐藤智之, 秋山泰, MEGADOCK
- Journal Title
  
  情報処理学会論文誌(TOM) 3(3)
  
  Pages: 91-106
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19300102
[Journal Article] Computer prediction of protein-protein interaction network using MEGADOCK -- application to systems biology.2010
- Author(s)
  Yuri Matsuzaki, Masahito Ohue, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama
- Journal Title
  
  TSUBAME e-Science Journal
  
  Volume: 2 Pages: 34-37
- Data Source
  KAKENHI-PROJECT-19300102
[Journal Article] Computer prediction of protein-protein interaction network using MEGADOCK-application to systems biology2010
- Author(s)
  Yuri Matsuzaki, Masahito Ohue, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama
- Journal Title
  
  TSUBAME e-Science Journal 2
  
  Pages: 34-37
- Data Source
  KAKENHI-PROJECT-19300102
[Journal Article] In silico classification of major clearance pathways of drugs with their physiochemical parameters.2010
- Author(s)
  Makiko Kusama, Kouta Toshimoto, Kazuya Maeda, Yuka Hirai, Satoki Imai, Koji Chiba, Yutaka Akiyama, Yuichi Sugiyama
- Journal Title
  
  Drug Metabolism and Disposition
  
  Volume: 28(8) Pages: 1362-1370
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19300102
[Journal Article] Exhaustive protein-protein interaction network prediction by using MEGADOCK2010
- Author(s)
  Yutaka Akiyama, Yuri Matsuzaki, Nobuyuki Uchikoga, Masahito Ohue
- Journal Title
  
  BioSupercomputing Newsletter 3
  
  Pages: 8-8
- Data Source
  KAKENHI-PROJECT-19300102
[Journal Article] MEGADOCK:立体構造情報からの網羅的タンパク質間相互作用予測とそのシステム生物学への応用2010
- Author(s)
  大上雅史, 松崎由理, 松崎裕介, 佐藤智之, 秋山泰
- Journal Title
  
  情報処理学会論文誌数理モデル化と応用(TOM)
  
  Volume: 3(3) Pages: 91-106
- NAID
  110007993887
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19300102
[Journal Article] Exhaustive protein-protein interaction network prediction by using MEGADOCK2010
- Author(s)
  Yutaka Akiyama, Yuri Matsuzaki, Nobuyuki Uchikoga, Masahito Ohue
- Journal Title
  
  BioSupercomputing Newsletter
  
  Volume: 3 Pages: 8-8
- Data Source
  KAKENHI-PROJECT-19300102
[Journal Article] In silico screening of protein-protein interactions with all-to-all rigid doc king and clustering : an application to pathway analysis2009
- Author(s)
  Yuri Matsuzaki, Yusuke Matsuzaki, Toshiyuki Sato, Yutaka Akiyama
- Journal Title
  
  Journal of Bioinformatics and Computational Biology 7(6)
  
  Pages: 991-1012
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19300102
[Journal Article] In silico screening of protein-protein interactions with all-to-all rigid docking and clustering : an application to pathway analysis2009
- Author(s)
  松崎由理, 松崎祐介, 佐藤智之, 秋山泰
- Journal Title
  
  Journal of Bioinformatics and Computational Biology 7(6)
  
  Pages: 991-1012
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19300102
[Journal Article] In silico screening of protein-protein interactions with all-to-all rigid docking and clustering: an application to pathway analysis2009
- Author(s)
  Yuri Matsuzaki, Yusuke Matsuzaki, Toshiyuki Sato, Yutaka Akiyama
- Journal Title
  
  Journal of Bioinformatics and Computational Biology 7(6)
  
  Pages: 991-1012
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19300102
[Journal Article] Development of an affinity evaluation and prediction system by using the shape complementarity characteristic between proteins2008
- Author(s)
  Koki Tsukamoto, Tatsuya Yoshikawa, Yuichiro Hourai, Kazuhiko Fukui, Yutaka Akiyama
- Journal Title
  
  Journal of Bioinformatics and Computational Biology 6(6)
  
  Pages: 1133-1156
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19300102
[Journal Article] Development of an affinity evaluation and prediction system by using the shape complementarity characteristic between proteins2008
- Author(s)
  Tsukamoto K, Yoshikawa T, Hourai Y, Fukui K, Akiyama Y
- Journal Title
  
  6
  
  Pages: 1133-1156
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17066002
[Journal Article] Development of an affinity evaluation and prediction system by using the shape complementarity characteristic between proteins2008
- Author(s)
  Y. Akiyama
- Journal Title
  
  Journal of Bioinformatics and Computational Biology 6(6)
  
  Pages: 1133-1156
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17066002
[Journal Article] evaluation and prediction system by using the shape complementarity characteristic between proteins2008
- Author(s)
  Koki Tsukamoto, Tatsuya Yoshikawa, Yuichiro Hourai, Kazuhiko Fukui, Yutaka Akiyama, Development of an affinity
- Journal Title
  
  Journal of Bioinformatics and Computational Biology 6(6)
  
  Pages: 1133-1156
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19300102
[Journal Article] High-throughput automated image processing system for cell array observations2008
- Author(s)
  Y. Akiyama
- Journal Title
  
  Information and Media Technologies 3(1)
  
  Pages: 71-78
- NAID
  110006453188
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17066002
[Journal Article] Development of an affinity evaluation and prediction system by using the shape complementarity characteristic between proteins2008
- Author(s)
  Koki Tsukamoto, Tatsuya Yoshikawa, Yuichiro Hourai, Kazuhiko Fukui, Yutaka Akiyama
- Journal Title
  
  Journal of Bioinformatics and Computational Biology 6 (6)
  
  Pages: 1133-1156
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19300102
[Journal Article] High-throughput automated image processing system for cell array observations2008
- Author(s)
  Tominaga D, Iguchi F, Horimoto K, Akiyama Y
- Journal Title
  
  Information and Media Technologies 3
  
  Pages: 71-78
- NAID
  110006453188
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17066002
[Journal Article] Optimization and Evaluation of Parallel Molecular Dynamics Simulation on Blue Gene/L2007
- Author(s)
  M. Sekijima J. Doi, T. Noguchi, Y. Akiyama, S. Shimizu
- Journal Title
  
  Proceedings of the IASTED International Conference on Parallel and Distributed Computer and Networks (PDCN2007) 1
  
  Pages: 257-262
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19300102
[Journal Article] Systematic Comparison of Catalytic Mechanisms of Hydrolysis and Transfer Reactions Classified in the EzCatDB Database2007
- Author(s)
  N.Nagano, T.Noguchi, Y.Akiyama
- Journal Title
  
  PROTEINS : Structure, Function, and Bioinformatics 66・1
  
  Pages: 147-159
- Data Source
  KAKENHI-PROJECT-17066002
[Journal Article] Development of automated image processing procedure for cell-arrays2007
- Author(s)
  Tominaga D, Iguchi F, Akiyama Y, Horimoto K
- Journal Title
  
  Proc. Of the 11th World Multi-Conference on Systemics, Cybernetics and Informatics (WMSCI2007) 4
  
  Pages: 19-24
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17066002
[Journal Article] Evaluation for interaction energy between glutamine and glutamine and various chemical compounds for developing the virtual screening system using quantum chemical calculations and molecular dynamics simulations2007
- Author(s)
  K.Tsukamoto, H.Shimizu, T.Ishida, Y.Akiyama, N.Nukina
- Journal Title
  
  WSEAS Transactions on Computers 6(4)
  
  Pages: 636-641
- Data Source
  KAKENHI-PROJECT-17066002
[Journal Article] Systematic Comparison of Catalytic Mechanisms of Hydrolysis and Transfer Reactions Classified in the EzCatDB Database2007
- Author(s)
  Nagano, N., Noguchi, T., Akiyama, Y.
- Journal Title
  
  PROTEINS: Structure, Function, and Bioin formatics 66(1)
  
  Pages: 147-159
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19300102
[Journal Article] Aggrigation mechanism of polyglutamine diseases revealed using quantum chemical calculations, fragment molecular orbital calculations, molecular dynamics simulations, and binding free energy calculations2006
- Author(s)
  K.Tsukamoto, H.Shimizu, T.Ishida, Y.Akiyama, N.Nukina
- Journal Title
  
  Journal of Molecular Structure : THEOCHEM 778(1-3)
  
  Pages: 85-95
- Data Source
  KAKENHI-PROJECT-17066002
[Journal Article] Fragmentation Studies of Peptide and Oligosaccharide using a Mid-IR Free Electron Laser2006
- Author(s)
  K.Fukui, Y.Akiyama, K.Takahashi
- Journal Title
  
  Journal of Japan Society for Laser Surgery and Medicine 27・2
  
  Pages: 92-96
- NAID
  10017644722
- Data Source
  KAKENHI-PROJECT-17066002
[Journal Article] Automated Docking of NADH to the Active Site of Nitric Oxide Reductase from Fusarium Oxysporum and Semi-empirical Calculations of the Electron Transfer Mechanism and the Hydrogen-bonding Network2006
- Author(s)
  K.Tsukamoto, Y.Akiyama
- Journal Title
  
  WSEAS Transactions on Computers 5・8
  
  Pages: 1701-1706
- Data Source
  KAKENHI-PROJECT-17066002
[Journal Article] Docking-calculation-based Method for Predicting Protein-RNA Interactions, Genome
- Author(s)
  大上雅史, 松崎由理, 秋山泰
- Journal Title
  
  Informatics in press
  
  Pages: 25-25
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] 住宅床ハウスダストの真菌叢に影響を及ぼす住環境因子に関する研究2023
- Author(s)
  渡辺麻衣子、伊澤和輝、橋本一浩、小林直樹、小沼ルミ、長谷川兼一、鍵直樹、川上裕司、秋山泰、山﨑朗子、工藤由起子、鎌田洋一、伊香賀俊治．
- Organizer
  日本マイコトキシン学会第 88 回学術講演会
- Data Source
  KAKENHI-PROJECT-21K10427
[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] 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] 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] ハウスダスト真菌叢解析と住環境比較2021
- Author(s)
  伊澤和輝、山﨑朗子、小林直樹、窪崎敦隆、鎌田洋一、長谷川兼一、工藤由起子、秋山泰、伊香賀俊治、渡辺麻衣子
- Organizer
  2021年室内環境学会学術大会
- Data Source
  KAKENHI-PROJECT-21K10427
[Presentation] マルチノード・マルチGPU上での網羅的なタンパク質間相互作用予測の高速化2020
- Author(s)
  渡辺紘生, 大上雅史, 秋山泰
- Organizer
  情報処理学会研究報告バイオ情報学（BIO）
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] 二次元分子記述子を用いた機械学習による環状ペプチドの細胞膜透過性予測2020
- Author(s)
  村田翔太朗, 山田雄太, 吉川寧, 大上雅史, 秋山泰
- Organizer
  情報処理学会研究報告バイオ情報学（BIO）
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] 共通な部分構造の再利用による高速なタンパク質リガンドドッキング手法の開発2020
- Author(s)
  久保田陸人, 柳澤渓甫, 吉川寧, 大上雅史, 秋山泰
- Organizer
  情報処理学会研究報告バイオ情報学（BIO）
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Machine Learning and Molecular Simulation on ABCI - Break Through a Bottleneck of Peptide Drug Discovery -2020
- Author(s)
  Akiyama Yutaka
- Organizer
  2nd RWBC-OIL Workshop
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] PKRank & SPDRank - Learning-to-rank methods for machine-learning-based drug discovery2020
- Author(s)
  Ohue Masahito, Suzuki Shogo D., Akiyama Yutaka
- Organizer
  Biophysical Society 64th Annual Meeting
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Improved protein-protein docking using arbitrary docking-derived protein interface predictions2020
- Author(s)
  Druyvesteyn Max, Ohue M,asahito Akiyama Yutaka
- Organizer
  2nd RWBC-OIL Workshop
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Prediction of membrane permeability and plasma protein binding of cyclic peptide drugs2020
- Author(s)
  Akiyama Yutaka
- Organizer
  The 5th IITM-Tokyo Tech Joint Symposium-Current trends in Bioinformatics: Big data analysis, machine learning and drug design
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Fragment Linking with DQN2020
- Author(s)
  Inagaki Masaya, Ohue Masahito, Akiyama Yutaka
- Organizer
  The 5th IITM-Tokyo Tech Joint Symposium-Current trends in Bioinformatics: Big data analysis, machine learning and drug design
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Development of fragment linking method for beyond rule of five2020
- Author(s)
  Tsushima Yuki, Ohue Masahito, Akiyama Yutaka
- Organizer
  The 5th IITM-Tokyo Tech Joint Symposium-Current trends in Bioinformatics: Big data analysis, machine learning and drug design
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] 縮アミノ酸を利用した二段階のシード探索によるメタゲノム配列相同性検索の改良2020
- Author(s)
  高畠和輝, 伊澤和輝, 秋川元宏, 大上雅史, 秋山泰
- Organizer
  情報処理学会研究報告バイオ情報学（BIO）
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Development of Membrane Permeability Prediction System for Cyclic Peptide: Large-Scale Molecular Dynamics Simulations2020
- Author(s)
  Sugiyama Satoshi, Yoshikawa Yasushi, Ohue Masahito, Akiyama Yutaka
- Organizer
  2nd RWBC-OIL Workshop
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Prediction of plasma protein binding for cyclic peptides by deep learning and molecular docking2020
- Author(s)
  Li Jianan, Yoshikawa Yasushi, Ohue Masahito, Akiyama Yutaka
- Organizer
  2nd RWBC-OIL Workshop
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Multidomain protein structure prediction using information about residues interacting on multimeric protein interfaces2020
- Author(s)
  Matsuno Shumpei, Ohue Masahito, Akiyama Yutaka
- Organizer
  2nd RWBC-OIL Workshop
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] 超高速タンパク質間相互作用予測システムMEGADOCK 5.0による細胞内タンパク質間相互作用の網羅的解明2020
- Author(s)
  秋山泰
- Organizer
  第41回AIセミナー - ABCIグランドチャレンジ2019成果報告会
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Multiple HPC Environments-Aware Container Image Configuration Workflow for Large-Scale All-to-All Protein-Protein Docking Calculations2020
- Author(s)
  Aoyama Kento, Watanabe Hiroki, Ohue Masahito, Akiyama Yutaka
- Organizer
  2nd RWBC-OIL Workshop
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Exhaustive protein-protein interaction prediction using MEGADOCK on a large-scale HPC environment2020
- Author(s)
  Watanabe Hiroki, Ohue Masahito, Akiyama Yutaka
- Organizer
  2nd RWBC-OIL Workshop
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Multiple HPC Environments-Aware Container Image Configuration for Bioinformatics Application2019
- Author(s)
  Aoyama Kento, Watanabe Hiroki, Ohue Masahito, Akiyama Yutaka
- Organizer
  International Conference for High Performance Computing, Networking, Storage, and Analysis (SC'19)
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] PKRank & SPDRank 化合物選別のためのランク学習法2019
- Author(s)
  大上雅史, 鈴木翔吾, 秋山泰
- Organizer
  生命情報科学若手の会第11回研究会
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] IT創薬と知財2019
- Author(s)
  秋山泰
- Organizer
  日本知財学会第17回年次学術研究発表会
- Invited
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Performance evaluation of MEGADOCK protein-protein interaction prediction system implemented with distributed containers on a cloud computing environment2019
- Author(s)
  Aoyama Kento, Yamamoto Yuki, Ohue Masahito, Akiyama Yutaka
- Organizer
  IPSJ Technical Report
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Performance evaluation of MEGADOCK protein?proteininteraction prediction system implemented with distributedcontainers on a cloud computing environment2019
- Author(s)
  Aoyama Kento, Yamamoto Yuki, Ohue Masahito, Akiyama Yutaka
- Organizer
  Parallel and Distributed Processing Techniques and Applications （PDPTA'19）
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] 機械学習を用いた環状ペプチドの膜透過性予測手法の開発2019
- Author(s)
  山田雄太, 吉川寧, 和久井直樹, 大上雅史, 秋山泰
- Organizer
  情報処理学会研究報告第57回バイオ情報学（BIO）
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Multiple HPC Environments-Aware Container Image Configuration for Bioinformatics Application2019
- Author(s)
  Aoyama Kento, Watanabe Hiroki, Ohue Masahito, Akiyama Yutaka
- Organizer
  第8回生命医薬情報学連合大会 (IIBMP2019)
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Accelerating MEGADOCK: protein-protein interaction prediction software on multiple nodes and multiple GPUs environment2019
- Author(s)
  Watanabe Hiroki, Ohue Masahito, Akiyama Yutaka
- Organizer
  第8回生命医薬情報学連合大会 (IIBMP2019)
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Parallelized pipeline for whole genome shotgun metagenomics with GHOSTZ-GPU and MEGAN2019
- Author(s)
  Masahito Ohue,Marina Yamasawa,Kazuki Izawa,Yutaka Akiyama
- Organizer
  In Proceedings of the 19th annual IEEE International Conference on Bioinformatics and Bioengineering (IEEE BIBE 2019)
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] 拡張サンプリング法による環状ペプチドの膜透過性予測システムの開発2019
- Author(s)
  黄毅聰, 吉川寧, 和久井直樹, 大上雅史, 秋山泰
- Organizer
  情報処理学会研究報告第57回バイオ情報学（BIO）
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] 機械学習を用いた環状ペプチドの体内安定性予測手法の改良2019
- Author(s)
  李佳男,吉川寧,大上雅史,秋山泰.
- Organizer
  情報処理学会研究報告バイオ情報学（BIO）
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Megadock-Web: an integrated database of high-throughput structure-based proteinprotein interaction predictions.2019
- Author(s)
  Ohue, Masahito, Hayashi Takanori, Matsuzaki Yuri, Yanagisawa Keisuke, Akiyama Yutaka
- Organizer
  Biophysical Society 63rd Annual Meeting
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] マルチドメインタンパク質の相互作用残基ペア予測を用いた立体構造予測手法の改良2019
- Author(s)
  松野駿平,大上雅史,秋山泰.
- Organizer
  情報処理学会研究報告バイオ情報学（BIO）
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Development of Membrane Permeability Prediction Method for Cyclic Peptids with Machine Learning2019
- Author(s)
  Yamada Yutaka, Yoshikawa Yasushi, Wakui Naoki, Ohue Masahito, Akiyama Yutaka
- Organizer
  第8回生命医薬情報学連合大会 (IIBMP2019)
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] 分子グラフ上の距離を考慮したグラフ畳込みニューラルネットワークによる化合物活性予測2019
- Author(s)
  伊井良太, 柳澤渓甫, 大上雅史, 秋山泰
- Organizer
  情報処理学会研究報告第57回バイオ情報学（BIO）
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Multidomain protein structure prediction using multimeric interaction residue pair information2019
- Author(s)
  Matsuno Shumpei, Ohue Masahito, Akiyama Yutaka
- Organizer
  第8回生命医薬情報学連合大会 (IIBMP2019)
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Acceleration and virtualization of parallel protein-protein interaction prediction system MEGADOCK2019
- Author(s)
  Ohue Masahito, Watanabe Hiroki, Aoyama Kento, Akiyama Yutaka
- Organizer
  The 57th Annual Meeting of the Biophysical Society of Japan
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Prediction of membrane permeability and plasma protein binding of cyclic peptides2019
- Author(s)
  Akiyama Yutaka
- Organizer
  AHeDD2019/IPAB2019 Joint Symposium
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Molecular activity prediction using graph convolutional deep neural network considering distance on a molecular graph2019
- Author(s)
  Ohue Masahito, Ii Ryota, Yanagisawa Keisuke, Akiyama Yutaka
- Organizer
  Parallel and Distributed Processing Techniques and Applications （PDPTA'19）
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Molecular activity prediction using graph convolutional deep neural network considering distance on a molecular graph2019
- Author(s)
  Ohue Masahito, Ii Ryota, Yanagisawa Keisuke, Akiyama Yutaka
- Organizer
  IPSJ Technical Report
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] PKRank & SPDRank: Learning-to-rank methods for ligand-based virtual screening2019
- Author(s)
  Ohue Masahito, Suzuki Shogo D., Akiyama Yutaka
- Organizer
  第8回生命医薬情報学連合大会 (IIBMP2019)
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] A playful tool for predicting protein-protein docking2019
- Author(s)
  Keren Jiang,Di Zhang,Tsubasa Iino,Risa Kimura,Tatsuo Nakajima,Kana Shimizu,Masahito Ohue,Yutaka Akiyama.
- Organizer
  Mobile and Ubiquitous Multimedia (MUM 2019)
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] 代表タンパク質構造群との構造アラインメントスコアプロファイルに基づくタンパク質間相互作用予測の高速化2019
- Author(s)
  林孝紀, 大上雅史, 秋山泰
- Organizer
  情報処理学会研究報告第57回バイオ情報学（BIO）
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] MEGADOCK-Web-Mito: a database of computer-predicted mitochondrial protein-protein interactions2018
- Author(s)
  Watanabe Hiroki, Hayashi Takanori, Ohue Masahito, Akiyama Yutaka
- Organizer
  1st RWBC-OIL Workshop, Tokyo Institute of Technology
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Efficient Hyperparameter Optimization by Using GP-MI Bayesian Optimization Algorithm for Predicting Drug-Target Interactions2018
- Author(s)
  Ban Tomohiro, Ohue Masahito, Akiyama Yutaka
- Organizer
  1st RWBC-OIL Workshop, Tokyo Institute of Technology
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] 生命情報解析分野におけるコンテナ型仮想化技術の動向と性能検証2018
- Author(s)
  青山建人, 大上雅史, 秋山泰
- Organizer
  情報処理学会研究報告第54回バイオ情報学（BIO）
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Performance Improvements of PPI Prediction Software by Tuning GPU Device Allocation on Multi-GPU Environments2018
- Author(s)
  Aoyama Kento, Ohue Masahito, Akiyama Yutaka
- Organizer
  第7回生命医薬情報学連合大会（IIBMP2018）
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Development of efficient protein-ligand docking method for virtual screening by reuse of fragments2018
- Author(s)
  Kubota Rikuto, Yanagisawa Keisuke, Ohue Masahito, Akiyama Yutaka
- Organizer
  1st RWBC-OIL Workshop, Tokyo Institute of Technology
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Hear the voice of structures: exhaustive protein-protein docking prediction and its application to drug discovery2018
- Author(s)
  Akiyama Yutaka
- Organizer
  International Conference on Bioinformatics 2018 (InCob2018), Delhi, India
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] 共通な部分構造の再利用アルゴリズムを用いたタンパク質リガンドドッキング手法の開発2018
- Author(s)
  久保田陸人, 柳澤渓甫, 大上雅史, 秋山泰
- Organizer
  情報処理学会研究報告第54回バイオ情報学（BIO）
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] 中分子IT創薬を加速する薬剤体内動態予測2018
- Author(s)
  秋山泰
- Organizer
  第22回オープンバイオ研究会
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] ミトコンドリアに関連したヒトタンパク質間相互作用予測データベースMEGADOCK-Web-Mitoの開発2018
- Author(s)
  渡辺紘生, 林孝紀, 大上雅史, 秋山泰
- Organizer
  情報処理学会研究報告第54回バイオ情報学（BIO）
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] MEGADOCK-Web: An Integrated Database of High-Throughput Structure-Based Protein-Protein Interaction Predictions2018
- Author(s)
  Masahito Ohue, Hayashi Takanori, Matsuzaki Yuri, Yanagisawa Keisuke, Akiyama Yutaka
- Organizer
  Biophysical Society 63rd Annual Meeting, Baltimore, MD, USA
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] 代表タンパク質構造群とのアラインメントを用いた高速なタンパク質間相互作用予測2018
- Author(s)
  林孝紀, 大上雅史, 秋山泰
- Organizer
  第7回生命医薬情報学連合大会（IIBMP2018）
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Feature extraction by enumerating lasso solutions for predicting plasma protein binding of peptide2018
- Author(s)
  akashi Tajimi, Naoki Wakui, Masahito Ohue, Yutaka Akiyama
- Organizer
  The Sixteenth Asia Pacific Bioinformatics Conference (APBC2018)
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15H02776
[Presentation] 複数のLasso回帰解に基づく解釈性の良い予測モデルを目指した環状ペプチド医薬品の体内安定性予測2018
- Author(s)
  多治見隆志, 和久井直樹, 大上雅史, 秋山泰
- Organizer
  情報処理学会研究報告第54回バイオ情報学（BIO）
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Feature extraction by enumerating lasso solutions for predicting plasma protein binding of peptide2018
- Author(s)
  Takashi Tajimi, Naoki Wakui, Masahito Ohue, Yutaka Akiyama
- Organizer
  The Sixteenth Asia Pacific Bioinformatics Conference (APBC2018)
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Comparison of the HPC Container Technologies for Bioinformatics Application2018
- Author(s)
  Aoyama Kento, Ohue Masahito, Akiyama Yutaka
- Organizer
  1st RWBC-OIL Workshop, Tokyo Institute of Technology
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] 大域的化合物特徴を表現するグラフ畳込みニューラルネットワーク2018
- Author(s)
  伊井良太, 柳澤渓甫, 大上雅史, 秋山泰
- Organizer
  第7回生命医薬情報学連合大会（IIBMP2018）
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] 中分子IT創薬を加速する薬剤体内動態予測2018
- Author(s)
  秋山泰
- Organizer
  第22回オープンバイオ研究会
- Data Source
  KAKENHI-PROJECT-15H02776
[Presentation] Computer prediction of plasma protein binding and membrane permeability of circular peptides as drug candidate2018
- Author(s)
  Akiyama Yutaka
- Organizer
  Asia Hub e-Drug Discovery Symposium (AHeDD2018), Korean Institute of Science and Technology Gangneung
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Link Mining for Kernel-based Compound-Protein Interaction Predictions Using a Chemogenomics Approach2017
- Author(s)
  Ohue M, Yamazaki T, Ban T, Akiyama Y.
- Organizer
  Intelligent Computing Theories and Application (In Proceedings of ICIC2017, Lecture Notes in Computer Science)
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Learning-to-rank based compound virtual screening by using pairwise kernel with multiple heterogeneous experimental data2017
- Author(s)
  Suzuki SD, Ohue M, Akiyama Y.
- Organizer
  In Proceedings of The 22nd International Symposium on Artificial Life and Robotics (AROB 2017)
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] Efficient Hyperparameter Optimization by Using Bayesian Optimization for Drug-Target Interaction Prediction2017
- Author(s)
  Ban T, Ohue M, Akiyama Y.
- Organizer
  In Proceedings of the 7th IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS 2017)
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] 標的タンパク質の立体構造を用いたリガンド候補化合物の上限サイズの推定による化合物フィルタリング2017
- Author(s)
  柳澤渓甫、大上雅史、石田貴士、秋山泰
- Organizer
  情報処理学会バイオ情報学研究会 2016-BIO-49(6)
- Place of Presentation
  沖縄科学技術大学院大学
- Year and Date
  2017-03-23
- Data Source
  KAKENHI-PROJECT-15H02776
[Presentation] 中分子IT創薬研究拠点(MIDL)の構想2017
- Author(s)
  秋山泰
- Organizer
  BioJapan2017
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] スーパーコンピューターと機械学習を用いた中分子創薬支援2017
- Author(s)
  秋山泰
- Organizer
  第1回TechPitch
- Invited
- Data Source
  KAKENHI-PROJECT-15H02776
[Presentation] インシリコスクリーニング技術を用いた抗シャーガス病の治療薬探索2017
- Author(s)
  吉野龍ノ介 , 安尾信明 , 萩原陽介 , 石田貴士 , 稲岡健 , 天野靖士 , 立石幸寛 , 大野一樹 , 生田目一寿 , 新美達也 , 折田正弥 , 北潔 , 秋山泰 , 関嶋政和
- Organizer
  第52回情報処理学会バイオ情報学研究会
- Data Source
  KAKENHI-PROJECT-15H02776
[Presentation] スーパーコンピューターと機械学習を用いた中分子創薬支援2017
- Author(s)
  秋山泰
- Organizer
  第1回TechPitch
- Data Source
  KAKENHI-PROJECT-17H01814
[Presentation] 標的タンパク質の立体構造を用いたリガンド候補化合物の上限サイズの推定による化合物フィルタリング2017
- Author(s)
  柳澤渓甫, 大上雅史, 石田貴士, 秋山泰
- Organizer
  情報処理学会バイオ情報学研究会　2017-BIO-49(6)
- Place of Presentation
  北陸先端科学技術大学院大学
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] フラグメント分割に基づく超高速化合物プレスクリーニング手法ESPRESSO2016
- Author(s)
  柳澤渓甫, 小峰駿汰, 鈴木翔吾, 大上雅史, 石田貴士, 秋山泰
- Organizer
  情報処理学会バイオ情報学研究会　2016-BIO-46(18)
- Place of Presentation
  沖縄科学技術大学院大学
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] SHAKE法に着目した分子動力学ソフトウェアmyPresto/OmegageneのCPU・GPU混在環境における高速化2016
- Author(s)
  後藤公太、笠原浩太、大上雅史、中村春木、秋山泰
- Organizer
  情報処理学会バイオ情報学研究会 2016-BIO-46(17)
- Place of Presentation
  沖縄科学技術大学院大学
- Data Source
  KAKENHI-PROJECT-15H02776
[Presentation] フラグメント分割に基づく超高速化合物プレスクリーニング手法ESPRESSO2016
- Author(s)
  柳澤渓甫、小峰駿太、鈴木翔吾、大上雅史、石田貴士、秋山泰
- Organizer
  情報処理学会バイオ情報学研究会 2016-BIO-46(18)
- Place of Presentation
  沖縄科学技術大学院大学
- Data Source
  KAKENHI-PROJECT-15H02776
[Presentation] タンパク質-化合物相互作用ネットワークのリンクマイニング2016
- Author(s)
  山崎卓朗, 大上雅史, 秋山泰
- Organizer
  情報処理学会研究報告
- Place of Presentation
  石川県能美市, JAIST
- Year and Date
  2016-03-19
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] GPUを用いたメタゲノム配列相同性解析ツールのMPI並列化と応用2016
- Author(s)
  藤井智也, 角田将典, 大上雅史, 石田貴士, 石原和幸, 秋山泰
- Organizer
  情報処理学会研究報告
- Place of Presentation
  石川県能美市, JAIST
- Year and Date
  2016-03-18
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] 活性値情報のグループ化とランク学習による化合物スクリーニング2016
- Author(s)
  鈴木翔吾, 大上雅史, 秋山泰
- Organizer
  情報処理学会バイオ情報学研究会　2016-BIO-46(26)
- Place of Presentation
  沖縄科学技術大学院大学
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] 活性値情報のグループ化とランク学習による化合物スクリーニング2016
- Author(s)
  鈴木翔吾、大上雅史、秋山泰
- Organizer
  情報処理学会バイオ情報学研究会 2016-BIO-46(26)
- Place of Presentation
  沖縄科学技術大学院大学
- Data Source
  KAKENHI-PROJECT-15H02776
[Presentation] SHAKE法に着目した分子動力学ソフトウェアmyPresto/OmegageneのCPU・GPU混在環境における高速化2016
- Author(s)
  後藤公太, 笠原浩太, 大上雅史, 中村春木, 秋山泰
- Organizer
  情報処理学会バイオ情報学研究会　2016-BIO-46(17)
- Place of Presentation
  沖縄科学技術大学院大学
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] タンパク質間相互作用予測結果データベース及び表示系の構築2016
- Author(s)
  長澤一輝, 松崎由理, 大上雅史, 秋山泰
- Organizer
  情報処理学会研究報告
- Place of Presentation
  石川県能美市, JAIST
- Year and Date
  2016-03-18
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] "GHOST-MP: an ultra-fast and high-sensitive homology search software for metagenome analysis"2015
- Author(s)
  Yutaka Akiyama
- Organizer
  3rd IIT Madras - Tokyo Tech Joint Symposium on Algorithms and Applications of Bioinformatics
- Place of Presentation
  IIT Madras, Chennai
- Year and Date
  2015-11-05
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] Analysis of protein docking decoys in terms of physicochemical properties of protein surfaces using rigid-body docking process2015
- Author(s)
  Nobuyuki Uchikoga, Yuri Matsuzaki, Masahito Ohue, Yutaka Akiyama
- Organizer
  3rd IIT Madras - Tokyo Tech Joint Symposium on Algorithms and Applications of Bioinformatics
- Place of Presentation
  IIT Madras, Chennai
- Year and Date
  2015-11-05
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] タンパク質ドッキングと配列情報特徴解析の融合によるタンパク質間相互作用予測の高精度化2015
- Author(s)
  小幡康文, 石田貴士, 秋山泰
- Organizer
  情報処理学会　第41回バイオ情報学研究会
- Place of Presentation
  北海道大学
- Year and Date
  2015-03-20
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] 既知の活性／非活性化合物のドッキング解析によるバーチャルスクリーニングに適したタンパク質立体構造モデルの選択2015
- Author(s)
  和久井直樹, 大上雅史, 千葉峻太朗, 石田貴士, 岩?博史, 秋山泰
- Organizer
  情報処理学会研究報告
- Place of Presentation
  沖縄県国頭郡, OIST
- Year and Date
  2015-06-25
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] SVMとDeep Learningに基づくヒトc-Yesキナーゼ阻害化合物の予測2015
- Author(s)
  鈴木翔吾, 柳澤渓甫, 大上雅史, 石田貴士, 秋山泰
- Organizer
  情報処理学会研究報告
- Place of Presentation
  沖縄県国頭郡, OIST
- Year and Date
  2015-06-24
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] Performance Analysis of MapReduce Implementations for High Performance Homology Search2015
- Author(s)
  Zhang Chaojie, Koichi Shirahata, Shuji Suzuki, Yutaka Akiyama, Satoshi Matsuoka
- Organizer
  HPCS2015
- Place of Presentation
  東京都文京区, 東京大学
- Year and Date
  2015-05-19
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] MEGADOCK: A high-performance protein-protein interaction prediction software for petascale supercomputing environments2015
- Author(s)
  Yuri Matsuzaki, Masahito Ohue, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama
- Organizer
  3rd IIT Madras - Tokyo Tech Joint Symposium on Algorithms and Applications of Bioinformatics
- Place of Presentation
  IIT Madras, Chennai
- Year and Date
  2015-11-05
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] フラグメント伸長型タンパク質-化合物ドッキングのビームサーチによる高速化2015
- Author(s)
  小峰駿汰, 石田貴士, 秋山泰
- Organizer
  情報処理学会研究報告
- Place of Presentation
  沖縄県国頭郡, OIST
- Year and Date
  2015-06-25
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] 低分子化合物二次元構造比較システムの改良2015
- Author(s)
  杉原舜, 石田貴士, 秋山泰
- Organizer
  情報処理学会研究報告
- Place of Presentation
  沖縄県国頭郡, OIST
- Year and Date
  2015-06-25
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] Drug clearance pathway prediction based on semi-supervised learning2015
- Author(s)
  Keisuke Yanagisawa，Takashi Ishida，Yuichi Sugiyama，Yutaka Akiyama
- Organizer
  情報処理学会　第41回バイオ情報学研究会
- Place of Presentation
  北海道大学
- Year and Date
  2015-03-20
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] Re-docking scheme to explore docking search space by using interaction profiles2014
- Author(s)
  Nobuyuki Uchikoga , Yuri Matsuzaki , Masahito Ohue , Takatsugu Hirokawa , Yutaka Akiyama
- Organizer
  Biophysical Society 58th Annual Meeting
- Place of Presentation
  Moscone Center, San Francisco
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] ハッシュテーブル及びde Bruijn Graphの分割による、ゲノム解析の消費メモリ量の低減2014
- Author(s)
  杉浦典和 , 石田貴士 , 秋山泰 , 関嶋政和
- Organizer
  情報処理学会第76回全国大会
- Place of Presentation
  東京都,　東京電機大学
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] 蛋白質-化合物ドッキングにおけるグリッドの分散配置による配座探索の改良2014
- Author(s)
  伴兼弘 , 石田貴士 , 秋山泰
- Organizer
  情報処理学会第37回バイオ情報学研究会
- Place of Presentation
  福岡県, 九州工業大学
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] Prediction of protein-protein interactions based on tertiary structures and transcription information2014
- Author(s)
  Yuri Matsuzaki , Nobuyuki Uchikoga , Masahito Ohue , Takashi Ishida , Yutaka Akiyama
- Organizer
  Biophysical Society 58th Annual Meeting
- Place of Presentation
  Moscone Center, San Francisco
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] Highly Precise Protein-Protein Interaction Prediction Based on Consensus Between Template-Based and de Novo Docking Methods2013
- Author(s)
  Masahito Ohue , Yuri Matsuzaki , Takehiro Shimoda , Takashi Ishida , Yutaka Akiyama
- Organizer
  Great Lakes Bioinformatics Conference 2013
- Place of Presentation
  Pittsburg, Pennsylvania, USA
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] De Bruijn Graphの分割によるVelvetの消費メモリの低減2013
- Author(s)
  杉浦典和 , 石田貴士 , 秋山泰 , 関嶋政和
- Organizer
  情報処理学会第36回バイオ情報学研究会
- Place of Presentation
  東京都, 東京工業大学
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] Protein-protein interaction prediction based on rigid-body docking with ultra-high-performance computing technique: applications to affinity prediction on CAPRI round 21 and interactome analyses2013
- Author(s)
  Masahito Ohue , Yuri Matsuzaki , Nobuyuki Uchikoga , Kohei Yamamoto , Takayuki Fujiwara , Takehiro Shimoda , Toshiyuki Sato , Takashi Ishida , Yutaka Akiyama
- Organizer
  CAPRI 2013 5th Evaluation Meeting
- Place of Presentation
  Utrecht, Netherland
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] NTDs創薬ターゲットタンパク質選択のためのデータベースiNTRODBの開発2013
- Author(s)
  石田貴士 , 蓮実梢 , 伴兼弘 , 秋山泰
- Organizer
  第54回日本熱帯医学会大会
- Place of Presentation
  長崎県, 長崎ブリックホール
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] MEGADOCK-GPU: Acceleration of Protein-Protein Docking Calculation on GPUs2013
- Author(s)
  Takehiro Shimoda , Takashi Ishida , Shuji Suzuki , Masahito Ohue , Yutaka Akiyama
- Organizer
  2nd International Workshop on Parallel and Cloud-based Bioinformatics and Biomedicine (ParBio2013), ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2013 (ACM-BCB 2013)
- Place of Presentation
  Bethesda, Maryland, USA
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] Sparse k-mer graphアルゴリズムの評価とVelvetへの実装2013
- Author(s)
  吉川舜亮 , 石田貴士 , 関嶋政和 , 秋山　泰
- Organizer
  情報処理学会第34回バイオ情報学研究会
- Place of Presentation
  沖縄県, 沖縄科学技術大学院大学
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] 結合自由エネルギー予測を用いたクリアランス経路予測の改善に関する研究2013
- Author(s)
  齊藤有紀 , 石田貴士 , 関嶋政和 , 秋山泰
- Organizer
  情報処理学会第34回バイオ情報学研究会
- Place of Presentation
  沖縄県, 沖縄科学技術大学院大学
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] 立体構造情報を用いたドッキング計算による大規模タンパク質-RNA間相互作用予測手法2011
- Author(s)
  大上雅史, 松崎由理, 秋山泰
- Organizer
  第73回情報処理学会全国大会
- Place of Presentation
  東京工業大学(東京)
- Year and Date
  2011-03-02
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] タンパク質とRNAの立体構造に基づいた網羅的計算による相互作用予測2011
- Author(s)
  大上雅史, 松崎由理, 内古閑伸之, 石田貴士, 秋山泰
- Organizer
  2011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(HPCS2011)
- Place of Presentation
  産業技術総合研究所(筑波)
- Year and Date
  2011-01-19
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] 相互作用プロファイルを用いたタンパク質間ドッキング問題における前処理の評価2011
- Author(s)
  内古閑伸之, 広川貴次, 秋山泰
- Organizer
  第3回バイオスーパーコンピューティングシンポジウム
- Place of Presentation
  甲南大学(神戸)
- Year and Date
  2011-02-21
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] タンパク質ドッキング計算結果の可視化とその解析2011
- Author(s)
  山本航平, 大上雅史, 松崎由理, 石田貴士, 秋山泰
- Organizer
  第73回情報処理学会全国大会
- Place of Presentation
  東京工業大学(東京)
- Year and Date
  2011-03-02
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] タンパク質-リガンド間の結合性解析の自動パイプライン化2011
- Author(s)
  尾渡裕成, 関嶋政和, 秋山泰
- Organizer
  第73回情報処理学会全国大会
- Place of Presentation
  東京工業大学(東京)
- Year and Date
  2011-03-02
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] MEGADOCKを用いたタンパク質間相互作用予測のシグナル伝達系への応用2011
- Author(s)
  松崎由理, 内古閑伸之, 大上雅史, 石田貴士, 秋山泰
- Organizer
  第3回バイオスーパーコンピューティングシンポジウム
- Place of Presentation
  甲南大学(神戸)
- Year and Date
  2011-02-21
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] In silico prediction of PPI network with structure-based all-to-all docking2010
- Author(s)
  Masahito Ohue, Yuri Matsuzaki, Yusuke Matsuzaki, Toshiyuki Sato, Yutaka Akiyama
- Organizer
  InCoB2010 - the 9th International Conference on Bioinformatics
- Place of Presentation
  早稲田大学(東京)
- Year and Date
  2010-09-26
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] A computational screening system of protein-protein interactions : connecting protein structural information to biological pathway estimation2010
- Author(s)
  松崎由理, 大上雅史, 松崎裕介, 佐藤智之, 秋山泰
- Organizer
  11th International Conference on Systems Biology (ICSB 2010)
- Place of Presentation
  Edinburgh Int'l Conference Centre(英国)
- Year and Date
  2010-10-12
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] MEGADOCK : An all-to all protein-protein interaction prediction system-Improving the sccuracy using boosting and binding energy reranking2010
- Author(s)
  Masahito Ohue, Yusuke Matsuzaki, Yuri Matsuzaki, Toshiyuki Sato, Yutaka Akiyama
- Organizer
  The 2nd Biosupercomputing Symposium (BSCS)
- Place of Presentation
  MY PLAZA ホール(東京)
- Year and Date
  2010-03-18
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] A computational screening system of protein-protein interactions : connecting protein structural information to biological pathway estimation2010
- Author(s)
  Yuri Matsuzaki, Masahito Ohue, Yusuke Matsuzaki, Toshiyuki Sato, Yutaka Akiyama
- Organizer
  11th International Conference on Systems Biology (ICSB 2010)
- Place of Presentation
  Edinburgh International Conference Centre (英国)
- Year and Date
  2010-10-12
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] リランキングを用いたタンパク質ドッキングの精度向上と網羅的タンパク質間相互作用予測への応用2010
- Author(s)
  大上雅史, 松崎裕介, 松崎由理, 佐藤智之, 秋山泰
- Organizer
  情報処理学会バイオ情報学研究会SIGBIO-20-3
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] A computatioal screening system of protein-ptotein interactions : connecting structural information to pathway estimation2010
- Author(s)
  Yuri Matsuzaki, Yusuke Matsuzaki, Masahito Ohue, Toshiyuki Sato, Yutaka Akiyama
- Organizer
  The 2nd Biosupercomputing Symposium (BSCS)
- Place of Presentation
  MY PLAZA ホール(東京)
- Year and Date
  2010-03-18
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] タンパク質の特性に基づく unbound ドッキングのための剛体予測手法の改良2010
- Author(s)
  松崎裕介, 大上雅史, 松崎由理, 佐藤智之, 関嶋政和, 秋山泰
- Organizer
  情処SIGBIO-20-4
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] タンパク質の特性に基づくunboundドッキングのための剛体予測手法の改良2010
- Author(s)
  松崎裕介, 大上雅史, 松崎由理, 佐藤智之, 関嶋政和, 秋山泰
- Organizer
  情報処理学会第20回バイオ情報学研究会
- Place of Presentation
  北陸先端大学(金沢)
- Year and Date
  2010-03-04
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] Exhaustive Protein-Protein Interaction Network Prediction by MEGADOCK2010
- Author(s)
  秋山泰
- Organizer
  Asia Hub for e-Drug Discovery Symposium AHeDD 2010
- Place of Presentation
  Yonsei University(韓国)(招待講演)
- Year and Date
  2010-12-18
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] Cluster analysis in post-docking process for rigid-body docking problem by using Interaction Fingerprints2010
- Author(s)
  Nobuyuki Uchikoga, Takatsugu Hirokawa, Yutaka Akiyama
- Organizer
  Computational Biology Research Center Workshop 2010 (CBRC2010)
- Place of Presentation
  産業技術総合研究所(東京)
- Year and Date
  2010-07-28
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] 単純ベイズ確率モデルの導入による天然変性蛋白質領域予測の改良2010
- Author(s)
  石田貴士, 秋山泰
- Organizer
  情報処理学会第21回バイオ情報学研究発表会
- Place of Presentation
  琉球大学(那覇)
- Year and Date
  2010-06-19
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] 立体構造情報を用いた網羅的計算によるタンパク質間相互作用ネットワーク予測2010
- Author(s)
  大上雅史, 松崎由理, 秋山泰
- Organizer
  生命情報科学若手の会第2回研究会
- Place of Presentation
  遺伝学研究所(三島)
- Year and Date
  2010-10-09
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] Searching near-native decoys from various types of protein complexes by cluster analysis with Interaction Finger Print2010
- Author(s)
  Nobuyuki Uchikoga, Takatsugu Hirokawa, Yutaka Akiyama
- Organizer
  The 48th Annual Meeting of the Biophysical Society of Japan
- Place of Presentation
  東北大学(仙台)
- Year and Date
  2010-09-22
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] A computational screening system of protein-protein interactions : connecting protein structural information to biological pathway estimation2010
- Author(s)
  Yuri Matsuzaki, Masahito Ohue, Yusuke Matsuzaki, Toshiyuki Sato, Yutaka Akiyama
- Organizer
  ETHZ - Tokyo Tech Workshop : Computing with GPUs, Cells, and Multicores
- Place of Presentation
  ETH Zurich (スイス)
- Year and Date
  2010-05-10
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] エネルギー計算に基づくリランキングとクラスタリングを用いた網羅的タンパク質間相互作用予測手法の提案2010
- Author(s)
  大上雅史, 松崎裕介, 松崎由理, 佐藤智之, 秋山泰
- Organizer
  第2回データ工学と情報マネジメントに関するフォーラム(DEIM2010)
- Place of Presentation
  淡路夢舞台国際会議場(淡路)
- Year and Date
  2010-03-01
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] Cluster analysis in post-docking process for rigid- body docking problem by using Interaction Fingerprints2010
- Author(s)
  Nobuyuki Uchikoga, Takatsugu Hirokawa, Yutaka Akiyama
- Organizer
  CBRC2010
- Place of Presentation
  Computational Biology Res.Center(東京)
- Year and Date
  2010-07-28
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] Exhaustive Protein-Protein Interaction Network Prediction by MEGADOCK2010
- Author(s)
  Yutaka Akiyama
- Organizer
  Asia Hub for eDrug Discovery (AHeDD) Symoposium 2010
- Place of Presentation
  Yonsei University (韓国) 招待講演
- Year and Date
  2010-12-18
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] A computational screening system of protein-protein interactions : connecting protein structural information to biological pathway estimation2010
- Author(s)
  松崎由理, 大上雅史, 松崎裕介, 佐藤智之, 秋山泰
- Organizer
  Computing with GPUs, Cells, and Multicores
- Place of Presentation
  ETH Zurich(スイス)
- Year and Date
  2010-05-10
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] Searching near-native decoys from various types of protein complexes by cluster analysis with Interaction Finger Print2010
- Author(s)
  Nobuyuki Uchikoga, Takatsugu Hirokawa, Yutaka Akiyama
- Organizer
  The 48th Annual Meeting of the Biophysical Soc.of Japan
- Place of Presentation
  Tohoku University(仙台)
- Year and Date
  2010-09-22
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] Exhaustive protein-protein interaction prediction with MEGADOCK and its application to signaling pathway estimation2010
- Author(s)
  Yuri Matsuzaki, Nobuyuki Uchikoga, Masahito Ohue, Takashi Ishida, Yutaka Akiyama
- Organizer
  Asia Hub for eDrug Discovery (AHeDD) Symoposium 2010
- Place of Presentation
  Yonsei University (韓国)
- Year and Date
  2010-12-18
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] リランキングを用いたタンパク質ドッキングの精度向上と網羅的タンパク質間相互作用予測への応用2010
- Author(s)
  大上雅史, 松崎裕介, 松崎由理, 佐藤智之, 秋山泰
- Organizer
  情報処理学会第20回バイオ情報学研究会
- Place of Presentation
  北陸先端大学(金沢)
- Year and Date
  2010-03-04
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] Post-docking analysis with interaction fingerprint2010
- Author(s)
  Nobuyuki Uchikoga, Takatsugu Hirokawa, Yutaka Akiyama
- Organizer
  Asia Hub for eDrug Discovery (AHeDD) Symoposium 2010
- Place of Presentation
  Yonsei University (韓国)
- Year and Date
  2010-12-18
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] Binding Analysis of Neuraminidase Inhibitors by Fragment Molecular Orbital Calculation2010
- Author(s)
  Yusei Owatari, Masakazu Sekijima, Yutaka Akiyama
- Organizer
  Asia Hub for eDrug Discovery (AHeDD) Symoposium 2010
- Place of Presentation
  Yonsei University (韓国)
- Year and Date
  2010-12-18
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] In silico prediction of PPI network with structure-based all-to-all docking2010
- Author(s)
  大上雅史, 松崎由理, 松崎裕介, 佐藤智之, 秋山泰
- Organizer
  InCoB2010-the 9th International Conference on Bioinformatics
- Place of Presentation
  Waseda University(東京)
- Year and Date
  2010-09-26
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] MEGADOCK:立体構造情報からの網羅的タンパク質間相互作用予測とそのシステム生物学への応用2010
- Author(s)
  大上雅史, 松崎由理, 松崎裕介, 佐藤智之, 秋山泰
- Organizer
  情報処理学会第78回数理モデル化と問題解決研究発表会
- Place of Presentation
  群馬大学(高崎)
- Year and Date
  2010-05-21
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] 相互作用プロファイルによるタンパク質複合体予測のポストドッキング解析2010
- Author(s)
  内古閑伸之, 広川貴次, 秋山泰
- Organizer
  第38回構造活性相関シンポジウム
- Place of Presentation
  徳島大学(徳島)
- Year and Date
  2010-10-30
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] タンパク質の特性に基づくunbound ドッキングのための剛体予測手法の改良2010
- Author(s)
  松崎裕介, 大上雅史, 松崎由理, 佐藤智之, 関嶋政和, 秋山泰
- Organizer
  情報処理学会第20回バイオ情報学研究会
- Place of Presentation
  北陸先端大学(金沢)
- Year and Date
  2010-03-04
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] A computational screening system of protein-protein interactions using tertiary structure data : an application to signaling pathway analysis2009
- Author(s)
  Yuri Matsuzaki, Yusuke Matsuzaki, Masahito Ohue, Toshiyuki Sato, Yutaka Akiyama
- Organizer
  BIOINFO 2009 CBI-KSBSB Joint Conference
- Place of Presentation
  Haeundae Grand Hotel(韓国)
- Year and Date
  2009-11-04
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] 分子動力学法に基づくタンパク質構造サンプリングとドッキング予測の改良2009
- Author(s)
  松崎裕介, 松崎由理, 関嶋政和, 秋山泰
- Organizer
  情報処理学会第18回バイオ情報学会研究会
- Place of Presentation
  北海道大学(札幌)
- Year and Date
  2009-09-17
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] Protein structure sampling based on molecular dynamics and improvement of docking prediction2009
- Author(s)
  Yusuke Matsuzaki, Yuri Matsuzaki, Masakazu Sekijima, Yutaka Akiyama
- Organizer
  BIOINFO 2009 CBI-KSBSB Joint Conference
- Place of Presentation
  Haeundae Grand Hotel(韓国)
- Year and Date
  2009-11-04
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] In silico screening of proteinprotein interactions with all-to-all rigid docking and clustering : an application to pathway analysis2009
- Author(s)
  松崎由理, 松崎裕介, 大上雅史, 佐藤智之, 秋山泰
- Organizer
  The 10th International Conference on Systems Biology (ICSB 2009)
- Place of Presentation
  Stanford University(米国)
- Year and Date
  2009-09-01
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] In silico screening of protein-protein interactions with all-to-all rigid doc king and clustering : an application to pathway analysis2009
- Author(s)
  Yuri Matsuzaki, Yusuke Matsuzaki, Masahito Ohue, Toshiyuki Sato, Yutaka Akiyama
- Organizer
  The 10th International Conference on Systems Biology (ICSB 2009)
- Place of Presentation
  Stanford大学(米国)
- Year and Date
  2009-09-01
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] Binding analysis of neuraminidase inhibitors by fragment MO calculation2009
- Author(s)
  Yusei Owatari, Masakazu Sekijima, Yutaka Akiyama
- Organizer
  BIOINFO 2009 CBI-KSBSB Joint Conference
- Place of Presentation
  Haeundae Grand Hotel(韓国)
- Year and Date
  2009-11-04
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] 物理化学的相互作用の導入による網羅的タンパク質間相互作用予測システムの高精度化2009
- Author(s)
  大上雅史, 松崎裕介, 松崎由理, 佐藤智之, 秋山泰
- Organizer
  情報処理学会第17回バイオ情報学会研究会
- Place of Presentation
  沖縄科学技術研究基盤整備機構(沖縄)
- Year and Date
  2009-05-26
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] ドッキング後処理によるPPI検出システムの応用と評価〜EGFRシグナル伝達系への適用にむけて2009
- Author(s)
  松崎由理, 松崎裕介, 大上雅史, 佐藤智之, 秋山泰
- Organizer
  第8回データ解析融合ワークショップ
- Place of Presentation
  学術総合センター(東京)
- Year and Date
  2009-03-16
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] Improvement of all-to-all protein-protein interaction prediction system MEGADOCK2009
- Author(s)
  大上雅史, 松崎裕介, 松崎由理, 秋山泰
- Organizer
  Genome Informatics Workshop (GIW2009)
- Place of Presentation
  Pacifico Yokohama(横浜)
- Year and Date
  2009-12-14
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] A GPGPU-based ultra fast computer system for mapping short DNA fragments onto human/mouse full genome sequence2009
- Author(s)
  Y. Akiyama
- Organizer
  The 3rd International Workshop on Approaches to Single-Cell Analysis (SCAW2008)
- Place of Presentation
  ETH (Zurich)
- Year and Date
  2009-09-11
- Data Source
  KAKENHI-PROJECT-17066002
[Presentation] Improvement of all-to-all protein-protein interaction prediction system MEGADOCK2009
- Author(s)
  Masahito Ohue, Yusuke Matsuzaki, Yuri Matsuzaki, Yutaka Akiyama
- Organizer
  BIOINFO 2009 CBI-KSBSB Joint Conference
- Place of Presentation
  Haeundae Grand Hotel(韓国)
- Year and Date
  2009-11-04
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] Improvement of all-to-all protein-protein interaction prediction system MEGADOCK2009
- Author(s)
  Masahito Ohue, Yusuke Matsuzaki, Yuri Matsuzaki, Yutaka Akiyama
- Organizer
  The 20th International Conference on Genome Informatics Workshop (GIW2009)
- Place of Presentation
  パシフィコ横浜(横浜)
- Year and Date
  2009-12-14
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] Fragment Mapping and Error Correction for Next-Generation Sequencers2009
- Author(s)
  Y. Akiyama
- Organizer
  第7回ライフサーベイヤシンポジウム
- Place of Presentation
  日立製作所中央研究所
- Year and Date
  2009-01-29
- Data Source
  KAKENHI-PROJECT-17066002
[Presentation] 物理化学的相互作用の導入によるタンパク質間相互作用予測システムの高精度化2009
- Author(s)
  大上雅史, 秋山泰
- Organizer
  第8回データ解析融合ワークショップ
- Place of Presentation
  学術総合センター(東京)
- Year and Date
  2009-03-16
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] A computational screening system of protein-protein interactions using tertiary structure data : with applicatio to pathway analysis2009
- Author(s)
  Yuri Matsuzaki, Yusuke Matsuzaki, Masahito Ohue, Toshiyuki Sato, Yutaka Akiyama
- Organizer
  Joint Computational Science Workshop 2009
- Place of Presentation
  理研横浜研究所(鶴見)
- Year and Date
  2009-07-09
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] 網羅的タンパク質間相互作用予測システムにおける判別精度の改良2009
- Author(s)
  大上雅史, 松崎裕介, 松崎由理, 秋山泰
- Organizer
  情報処理学会第18回バイオ情報学会研究会
- Place of Presentation
  北海道大学(札幌)
- Year and Date
  2009-09-17
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] フラグメントMO法によるノイラミニダーゼ阻害薬の結合性解析2009
- Author(s)
  尾渡裕成, 関嶋政和, 秋山泰
- Organizer
  情報処理学会第18回バイオ情報学会研究会
- Place of Presentation
  北海道大学(札幌)
- Year and Date
  2009-09-17
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] 物理化学的相互作用の導入による網羅的タンパク質間相互作用予測システムの高精度化2009
- Author(s)
  大上雅史, 松崎裕介, 松崎由理, 佐藤智之, 秋山泰
- Organizer
  情処SIGBIO-17-4
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] Predicting protein-protein interactions with a peta-flops computer : Techniques and potential applications to systems biology research2008
- Author(s)
  Yutaka Akiyama, Yuri Matsuzaki, Yusuke Matsuzaki, Toshiyuki Sato, Satoshi Matsuoka
- Organizer
  The ninth international conference of KSBSB (Bioinfo2008)
- Place of Presentation
  忠北大学校(韓国)
- Year and Date
  2008-11-13
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] Virtual screening of protein-protein interactions : an application to known signal transduction systems2008
- Author(s)
  Yuri Matsuzaki, Yusuke Matsuzaki, Toshiyuki Sato, Yutaka Akiyama
- Organizer
  The 2008 Annual Conference of the Japanese Society for Bioinformatics (JSBi2008)
- Place of Presentation
  千里ライフサイエンスセンター(大阪)
- Year and Date
  2008-12-15
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] Megadock - a rapid screening system for all-to-all protein docking analysis with precalculated fourier library of protein structures2008
- Author(s)
  Yutaka Akiyama, Toshiyuki Sato, Yusuke Matsuzaki, Yuri Matsuzaki
- Organizer
  The 2008 Annual Conference of the Japanese Society for Bioinformatics (JSBi2008)
- Place of Presentation
  千里ライフサイエンスセンター(大阪)
- Year and Date
  2008-12-15
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] MEGADOCK - A massively parallel software system for all-to-all protein docking analysis with pre-calculated Fourier library of protein structures2008
- Author(s)
  Yutaka Akiyama, Toshiyuki Sato, Yusuke Matsuzaki, Yuri Matsuzaki
- Organizer
  バイオスーパーコンピューティング・シンポジウム(BSCS)2008
- Place of Presentation
  丸の内マイプラザ(東京)
- Year and Date
  2008-12-25
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] Megadock - a rapid screening system for all-to-all protein docking analysis with pre-calculated fourier library of protein structures2008
- Author(s)
  Yutaka Akiyama, Toshiyuki Sato, Yusuke Matsuzaki, Yuri Matsuzaki
- Organizer
  1st Joint Workshop on Computational Science
- Place of Presentation
  理化学研究所(和光)
- Year and Date
  2008-07-07
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] A GPGPU-based ultra fast computer system for mapping short DNA fragments onto human/ mouse full genome sequence2008
- Author(s)
  Y. Akiyama
- Organizer
  The 2008 Annual Coniference of the Japanese Society for Bioinformatics (JSBi2008)
- Place of Presentation
  千里ライフサイエンスセンター(大阪)
- Year and Date
  2008-12-15
- Data Source
  KAKENHI-PROJECT-17066002
[Presentation] In Silico Screening Method of Protein-protein Interactions Using All-to-all Rigid Docking and Clustering : with Application to Pathway Analysis2008
- Author(s)
  Yuri Matsuzaki, Yusuke Matsuzaki, Toshiyuki Sato, Yutaka Akiyama
- Organizer
  バイオスーパーコンピューティング・シンポジウム(BSCS)2008
- Place of Presentation
  丸の内マイプラザ(東京)
- Year and Date
  2008-12-25
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] A GPGPU-based ultra fast sequence comparison system for mapping short DNA fragments onto human/ mouse full genome sequence fragments onto human/mouse full genome sequence2008
- Author(s)
  Y. Akiyama
- Organizer
  AHeDD2008/IPAB2008 Joint Symposium
- Place of Presentation
  恵比寿ガーデンプレイス(東京)
- Year and Date
  2008-10-16
- Data Source
  KAKENHI-PROJECT-17066002
[Presentation] タンパク質ドッキング予測プログラムによるシグナル伝達系のタンパク質間相互作用解析2008
- Author(s)
  松崎由理, 松崎裕介, 佐藤智之, 秋山泰
- Organizer
  情報処理学会第13回バイオ情報学研究会
- Place of Presentation
  琉球大学(沖縄)
- Year and Date
  2008-06-26
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] タンパク質間相互作用予測のためのドッキング後処理システムの開発2008
- Author(s)
  松崎裕介, 松崎由理, 佐藤智之, 秋山泰
- Organizer
  情報処理学会第13回バイオ情報学研究会
- Place of Presentation
  琉球大学(沖縄)
- Year and Date
  2008-06-26
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] Megadock-a rapid screening system for all-to-all protein docking analysis with precalculated fourier library of protein structures2008
- Author(s)
  秋山泰, 佐藤智之, 松崎裕介, 松崎由理
- Organizer
  The 2008 Annual Conference of the Japanese Society for Bioinformatics(JSBi2008)
- Place of Presentation
  千里ライフサイエンスセンター(大阪
- Year and Date
  2008-12-15
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] Analysis of protein・protein interactions of signal transduction pathways using a docking prediction program2008
- Author(s)
  Yuri Matsuzaki, Yusuke Matsuzaki, Toshiyuki Sato, Yutaka Akiyama
- Organizer
  1st Joint Workshop on Computational Science
- Place of Presentation
  理化学研究所(和光)
- Year and Date
  2008-07-07
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] Development of post・docking system for protein-protein interaction prediction2008
- Author(s)
  Yusuke Matsuzaki, Yuri Matsuzaki, Toshiyuki Sato, Yutaka Akiyama
- Organizer
  1st Joint Workshop on Computational Science
- Place of Presentation
  理化学研究所(和光)
- Year and Date
  2008-07-07
- Data Source
  KAKENHI-PROJECT-19300102
[Presentation] パイロシーケンシング法における読み取りエラー発生シミュレータとその応用2008
- Author(s)
  秋山泰
- Organizer
  第6回ライフサーベイヤシンポジウム
- Place of Presentation
  大阪大学
- Year and Date
  2008-06-26
- Data Source
  KAKENHI-PROJECT-17066002
[Presentation] システム生物学と創薬2007
- Author(s)
  秋山泰
- Organizer
  第21回日本薬物動態学会ワークショップ
- Place of Presentation
  昭和大学、東京
- Year and Date
  2007-04-12
- Data Source
  KAKENHI-PROJECT-17066002
[Presentation] Large-scale computing for bioinformatics2000
- Author(s)
  Akiyama Y
- Organizer
  Virtual Laboratory based on Grid Technology Workshop
- Place of Presentation
  Seoul, Korea
- Year and Date
  2000-03-24
- Data Source
  KAKENHI-PROJECT-17066002
[Presentation] Improvement of the Protein-Protein Docking Prediction by Introducing a Simple Hydrophobic Interaction Model: an Application to Interaction Pathway Analysis
- Author(s)
  Ohue M, Matsuzaki Y, Ishida T, Akiyama Y
- Organizer
  The 7th IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB 2012)
- Place of Presentation
  東京工業大学（東京）
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] 半教師付き学習を用いた薬物クリアランス経路予測
- Author(s)
  柳澤渓甫, 石田貴士, 秋山泰
- Organizer
  情報処理学会　第38回バイオ情報学研究会
- Place of Presentation
  沖縄科学技術大学院大学
- Year and Date
  2014-06-25 – 2014-06-27
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] パスウェイ情報を用いた顧みられない熱帯病創薬支援のための統合データベースiNTRODBの改良
- Author(s)
  蓮実　梢, 石田貴士, 秋山泰
- Organizer
  情報処理学会　第38回バイオ情報学研究会
- Place of Presentation
  沖縄科学技術大学院大学
- Year and Date
  2014-06-25 – 2014-06-27
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] 簡易疎水性相互作用モデルによるタンパク質間ドッキング予測の高精度化
- Author(s)
  藤原隆之, 松崎由理，石田貴士，秋山泰
- Organizer
  情報処理学会研究報告 2012-BIO-29(21)
- Place of Presentation
  沖縄科学技術大学院大学（沖縄）
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] タンパク質間ドッキング予測における実空間での効率的な評価スコア計算方法の研究
- Author(s)
  下田雄大，石田貴士，秋山泰
- Organizer
  情報処理学会研究報告 2012-BIO-29(20)
- Place of Presentation
  沖縄科学技術大学院大学（沖縄）
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] MEGADOCKを用いたタンパク質間相互作用予測のヒトアポトーシスパスウェイ解析への応用
- Author(s)
  大上雅史，松崎由理，石田貴士，秋山泰
- Organizer
  情報処理学会研究報告 2012-BIO-32(13)
- Place of Presentation
  京都大学桂キャンパス（京都）
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] タンパク質間ドッキング予測における機械学習を用いた目的関数の動的調整
- Author(s)
  大上雅史，石田貴士，秋山泰
- Organizer
  情報処理学会研究報告 2012-BIO-29(19)
- Place of Presentation
  沖縄科学技術大学院大学（沖縄）
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] 大規模GPUクラスタによるタンパク質ドッキング計算システム
- Author(s)
  大上雅史,下田雄大,松崎由理,石田貴士,秋山泰
- Organizer
  情報処理学会　第38回バイオ情報学研究会
- Place of Presentation
  沖縄科学技術大学院大学
- Year and Date
  2014-06-25 – 2014-06-27
- Data Source
  KAKENHI-PROJECT-24240044
[Presentation] 構造情報に基づくタンパク質間相互作用ネットワーク予測精度の改善
- Author(s)
  山本航平，大上雅史，石田貴士，秋山泰
- Organizer
  情報処理学会研究報告 2012-BIO-32(14)
- Place of Presentation
  京都大学（京都）
- Data Source
  KAKENHI-PROJECT-24240044

1. TSUKAMOTO Koki (90399501)

# of Collaborated Projects: 2 results

# of Collaborated Products: 3 results
2. SEKIJIMA MASAKAZU (80371053)

# of Collaborated Projects: 2 results

# of Collaborated Products: 9 results
3. KAMBARA Hideki (20397011)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
4. TAKEYAMA Haruko (60262234)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
5. SHIKU Hitoshi (10361164)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
6. KOBATAKE Eiri (00225484)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
7. OKAMURA Yoshiko (80405513)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
8. ISHIKAWA Yutaka (70345122)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
9. SATO Mitsuhisa (60333481)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
10. BOKU Taisuke (90209346)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
11. MATSUBA Hiroya (30444095)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
12. Osaka Hitoshi (90426320)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
13. 瀬々潤 (40361539)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
14. 平山謙二 (60189868)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
15. 大上雅史 (50743209)

# of Collaborated Projects: 1 results

# of Collaborated Products: 57 results
16. 山口雄輝 (50345360)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
17. 渡辺麻衣子 (00432013)

# of Collaborated Projects: 1 results

# of Collaborated Products: 2 results
18. 伊澤和輝 (50803813)

# of Collaborated Projects: 1 results

# of Collaborated Products: 2 results
19. 柳澤渓甫 (40866646)

# of Collaborated Projects: 1 results

# of Collaborated Products: 5 results
20. Kita Kiyoshi

# of Collaborated Projects: 1 results

# of Collaborated Products: 2 results
21. 千見寺浄慈

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
22. 松崎由理

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
23. 上田卓見

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

Akiyama Yutaka 秋山 泰

AKIYAMA Yutaka 秋山 泰

Research Projects

Research Products

Co-Researchers

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

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Research on the relevance between fungal growth and mite population

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Elucidation of the mechanism of mitochondrial disease cell death inhibition and drug discovery

Principal Investigator

Project Period (FY)

Research Category

Review Section

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Development of computational methods for supporting druggable cyclic peptide designPrincipal Investigator

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In silico, in vitro, X-ray crystallography, and integrated strategies for discovering spermidine synthase inhibitors for Chagas disease

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Computational drug discovery techniques with systematic target identification and high-performance molecular simulationPrincipal Investigator

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An exhaustive all-to-all protein-protein interaction prediction algorithm based on 3-D shape complimentarity and its statistical distribution on protein surface.Principal Investigator

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Large Virtual Memory Space Supporting System on Next Generation PC Clusters

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The development of accurate quantitative and digital tools for Lifesurveyor

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[Book] 一細胞定量解析の最前線-ライフサーベイヤ構築に向けて-(シーエムシー出版)2006

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

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[Journal Article] Amide-to-ester substitution as a stable alternative to N-methylation for increasing membrane permeability in cyclic peptides.2023

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

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

Akiyama Yutaka 秋山泰

AKIYAMA Yutaka 秋山泰