Masahito Ohue

Profile Information

Affiliation: Associate Professor, Department of Computer Science, School of Computing, Tokyo Institute of Technology

Degree: 博士（工学）(東京工業大学)

Researcher number: 50743209
ORCID ID: https://orcid.org/0000-0002-0120-1643
J-GLOBAL ID: 201301038375117396
researchmap Member ID: B000228610

External link: http://goo.gl/Y4LG1

並列計算機を活用した生命情報科学や計算創薬の研究を行っています．

Research Interests

Research Areas

Research History

Jan, 2024 - Present

Associate Professor, Department of Computer Science, School of Computing, Tokyo Institute of Technology
Apr, 2016 - Dec, 2023

Assistant Professor, School of Computing, Tokyo Institute of Technology
Apr, 2016 - Mar, 2020

Advanced Computational Drug Discovery Unit, Institute of Innovative Research, Tokyo Institute of Technology
Apr, 2015 - Mar, 2016

Assistant Professor, Graduate School of Information Science and Engineering, Tokyo Institute of Technology
Apr, 2014 - Mar, 2015

Tokyo Institute of Technology Research Fellow
Apr, 2014 - Mar, 2015

JSPS Research Fellow PD
Apr, 2011 - Mar, 2014

JSPS Research Fellow DC1

Education

Apr, 2011 - Mar, 2014

Dept. of Computer Sci., Doctor's course, Grad. School of Info. Sci. and Eng., Tokyo Institute of Technology
Apr, 2009 - Mar, 2011

Dept. of Computer Sci., Master's course, Grad. School of Info. Sci. and Eng., Tokyo Institute of Technology
Apr, 2007 - Mar, 2009

Dept. of Computer Sci., Fac. of Engineering, Tokyo Institute of Technology
Apr, 2002 - Mar, 2007

Dept. of Electronics and Information Eng., Ishikawa National College of Technology

Awards

Oct, 2023

CBI学会若手奨励賞, 特定非営利活動法人CBI学会
Jun, 2022

第35回安藤博記念学術奨励賞, 一般財団法人安藤研究所

大上雅史
Mar, 2022

2021年度（令和3年度）山下記念研究賞, 一般社団法人情報処理学会

大上雅史
Apr, 2021

バイオ情報学研究会優秀プレゼンテーション賞, 一般社団法人情報処理学会

大上雅史
Oct, 2020

Oxford Journals - JSBi Prize, 日本バイオインフォマティクス学会

大上雅史
Apr, 2019

平成31年度科学技術分野の文部科学大臣表彰若手科学者賞, 文部科学省

大上雅史
Sep, 2018

Early Career Presentation Award, Biophysical Society of Japan
Aug, 2018

Tokyo Tech Challenging Research Award, Tokyo Institute of Technology
Mar, 2018

Funai Research Award for Young Scientist, The Funai Foundation for Information Technology (FFIT)
Feb, 2015

Tejima Memorial Research Award

Masahito Ohue
Feb, 2014

Fourth (FY2013) JSPS Ikushi Prize, Japan Society for the Promotion of Science

Masahito Ohue
Mar, 2011

The 73rd IPSJ Conference Student Award, IPSJ

Masahito Ohue
Jun, 2010

The 78th IPSJ SIGMPS Presentation Award, IPSJ

Masahito Ohue
Mar, 2010

DEIM2010 Excellent Student Presentation Award, DBSJ

Masahito Ohue
Mar, 2010

2009 IPSJ SIGBIO Best Student Presentation Award, IPSJ

Masahito Ohue
Sep, 2006

IEICE Hokuriku Excellent Student Presentation Award, IEICE

Masahito Ohue

Major Committee Memberships

Mar, 2020 - Present

理事, 特定非営利活動法人日本バイオインフォマティクス学会
Apr, 2019 - Present

理事, 特定非営利活動法人並列生物情報処理イニシアティブ
Apr, 2015 - Jun, 2021

理事, 一般社団法人日本生物物理学会

Papers

Generating Potential Protein-Protein Interaction Inhibitor Molecules Based on Physicochemical Properties.

Masahito Ohue, Yuki Kojima, Takatsugu Kosugi

Molecules (Basel, Switzerland), 28(15), Jul 26, 2023
CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides.

Jianan Li, Keisuke Yanagisawa, Masatake Sugita, Takuya Fujie, Masahito Ohue, Yutaka Akiyama

Journal of chemical information and modeling, 63(7) 2240-2250, Apr 10, 2023
Editorial: Web tools for modeling and analysis of biomolecular interactions Volume II.

Jessica Andreani, Brian Jiménez-García, Masahito Ohue

Frontiers in molecular biosciences, 10 1190855-1190855, 2023
Lipid Composition Is Critical for Accurate Membrane Permeability Prediction of Cyclic Peptides by Molecular Dynamics Simulations.

Masatake Sugita, Takuya Fujie, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama

Journal of chemical information and modeling, 62(18) 4549-4560, Sep 26, 2022
Effective Protein-Ligand Docking Strategy via Fragment Reuse and a Proof-of-Concept Implementation.

Keisuke Yanagisawa, Rikuto Kubota, Yasushi Yoshikawa, Masahito Ohue, Yutaka Akiyama

ACS omega, 7(34) 30265-30274, Aug 30, 2022
Solubility-Aware Protein Binding Peptide Design Using AlphaFold.

Takatsugu Kosugi, Masahito Ohue

Biomedicines, 10(7), Jul 7, 2022
Plasma protein binding prediction focusing on residue-level features and circularity of cyclic peptides by deep learning.

Jianan Li, Keisuke Yanagisawa, Yasushi Yoshikawa, Masahito Ohue, Yutaka Akiyama

Bioinformatics (Oxford, England), 38(4) 1110-1117, Jan 27, 2022
Editorial: Web Tools for Modeling and Analysis of Biomolecular Interactions.

Jessica Andreani, Masahito Ohue, Brian Jiménez-García

Frontiers in molecular biosciences, 9 875859-875859, 2022
Quantitative Estimate Index for Early-Stage Screening of Compounds Targeting Protein-Protein Interactions.

Takatsugu Kosugi, Masahito Ohue

International journal of molecular sciences, 22(20), Oct 10, 2021
Improved Large-Scale Homology Search by Two-Step Seed Search Using Multiple Reduced Amino Acid Alphabets.

Kazuki Takabatake, Kazuki Izawa, Motohiro Akikawa, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama

Genes, 12(9), Sep 21, 2021
Large-Scale Membrane Permeability Prediction of Cyclic Peptides Crossing a Lipid Bilayer Based on Enhanced Sampling Molecular Dynamics Simulations.

Masatake Sugita, Satoshi Sugiyama, Takuya Fujie, Yasushi Yoshikawa, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama

Journal of chemical information and modeling, 61(7) 3681-3695, Jul 26, 2021
Taxonomic and Gene Category Analyses of Subgingival Plaques from a Group of Japanese Individuals with and without Periodontitis.

Kazuki Izawa, Kazuko Okamoto-Shibayama, Daichi Kita, Sachiyo Tomita, Atsushi Saito, Takashi Ishida, Masahito Ohue, Yutaka Akiyama, Kazuyuki Ishihara

International journal of molecular sciences, 22(10), May 18, 2021
MEGADOCK-GUI: a GUI-based complete cross-docking tool for exploring protein-protein interactions.

Masahito Ohue, Yutaka Akiyama

CoRR, abs/2105.03617, 2021
Structural Basis for the Binding Mechanism of Human Serum Albumin Complexed with Cyclic Peptide Dalbavancin.

Sho Ito, Akinobu Senoo, Satoru Nagatoishi, Masahito Ohue, Masaki Yamamoto, Kouhei Tsumoto, Naoki Wakui

Journal of medicinal chemistry, 63(22) 14045-14053, Nov 25, 2020
Evaluation of CONSRANK-Like Scoring Functions for Rescoring Ensembles of Protein-Protein Docking Poses.

Guillaume Launay, Masahito Ohue, Julia Prieto Santero, Yuri Matsuzaki, Cécile Hilpert, Nobuyuki Uchikoga, Takanori Hayashi, Juliette Martin

Frontiers in molecular biosciences, 7 559005-559005, 2020
Multiple HPC Environments-Aware Container Image Configuration Workflow for Large-Scale All-to-All Protein–Protein Docking Calculations

Kento Aoyama, Hiroki Watanabe, Masahito Ohue, Yutaka Akiyama

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 12082 LNCS 23-39, 2020
Development of computational pipeline software for genome/exome analysis on the K computer

Kento Aoyama, Masanori Kakuta, Yuri Matsuzaki, Takashi Ishida, Masahito Ohue, Yutaka Akiyama

Supercomputing Frontiers and Innovations, 7(1) 37-54, Jan 1, 2020
Multidomain protein structure prediction using information about residues interacting on multimeric protein interfaces.

Shumpei Matsuno, Masahito Ohue, Yutaka Akiyama

Biophysics and physicobiology, 17 2-13, 2020
Multidomain protein structure prediction using information about residues interacting on multimeric protein interfaces.

Shumpei Matsuno, Masahito Ohue, Yutaka Akiyama

Biophysics and physicobiology, 17 2-13, 2020
High-performance cloud computing for exhaustive protein-protein docking.

Masahito Ohue, Kento Aoyama, Yutaka Akiyama

CoRR, abs/2006.08905, 2020

Research Projects

天然物が織り成す化合物潜在空間が拓く生物活性分子デザイン

科学研究費助成事業, 学術変革領域研究(A), 日本学術振興会, Apr, 2023 - Mar, 2028

菊地和也, 榊原康文, 伊藤寛晃, 丹羽節, 荒井緑, 大森建, 大上雅史, 上田実, 鎌田真由美, 吉田稔
Latent Chemical Space for Beyond Rule-of-Five Compounds

Grants-in-Aid for Scientific Research, Grant-in-Aid for Transformative Research Areas (A), Japan Society for the Promotion of Science, Apr, 2023 - Mar, 2028
マルチモダリティ創薬を拓くインフォマティクス基盤

戦略的な研究開発の推進創発的研究支援事業, 科学技術振興機構, Apr, 2022 - 2028

大上雅史
Functional analysis of slit diaphragm associated protein, MAGI-2, and development of a novel CKD therapeutic agent

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (B), Japan Society for the Promotion of Science, Apr, 2023 - Mar, 2026
Development of a Protein-Cyclic Peptide Complex Structure Database and Advanced Molecular Design Approaches

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (B), Japan Society for the Promotion of Science, Apr, 2023 - Mar, 2026
Taming "untamed" generative AIs by developing compound optimization support tools that enable the interactive use of domain knowledge in medicinal chemistry

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (C), Japan Society for the Promotion of Science, Apr, 2022 - Mar, 2025
Development of a computational drug design method for targeting protein-protein interactions

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (B), Japan Society for the Promotion of Science, Apr, 2020 - Mar, 2023
大規模分子シミュレーションによるインシリコスクリーニング支援と構造インフォマティクス技術の高度化

創薬等ライフサイエンス研究支援基盤事業, 日本医療研究開発機構, Apr, 2017 - Mar, 2022

関嶋政和
タンパク質を制御するペプチドのデザインAI

戦略的な研究開発の推進戦略的創造研究推進事業 ACT-X, 科学技術振興機構, Apr, 2020 - 2022

大上雅史
ミトコンドリアを取り巻く未知のインタラクトームの予測と実証

科研費若手研究, 日本学術振興会, Apr, 2018 - Mar, 2021

大上雅史
ヒューマンコンピュテーションと計算創薬の融合的実装による創薬計算科学の深化

科研費基盤研究(C), 日本学術振興会, Apr, 2018 - Mar, 2020

山本一樹
中分子創薬に適した特性を有する環状ペプチド分子設計手法の開発

科研費基盤研究(B), 日本学術振興会, Apr, 2017 - Mar, 2020

秋山泰
CHOKO: Clustering of High thrOughput in silico protein-protein docKing - investigation of hub prOteins

二国間交流事業共同研究 SAKURAプログラム, 日本学術振興会-フランス外務省MAEDI, Apr, 2017 - Mar, 2019

大上雅史
Technology of a medium-scale peptide-protein interaction analysis

Grant-in-Aid for Scientific Research (C), JSPS, Apr, 2015 - Mar, 2018

Nobuyuki Uchikoga
Technology of a medium-scale peptide-protein interaction analysis

Grant-in-Aid for Young Scientists (B), JSPS, Apr, 2015 - Mar, 2018

Masahito Ohue
Parallel Computing System for Drug Target Discovery based on Protein-Protein Interaction Predictions

Grant-in-Aid for JSPS Fellows, JSPS, Apr, 2014 - Mar, 2015

Masahito Ohue
An all-to-all protein-protein interaction prediction system with tertiary structure information

Grant-in-Aid for JSPS Fellows, JSPS, Apr, 2011 - Mar, 2014

Masahito Ohue

Misc.

AIによって変わる生命科学—特集科学の新たなパラダイム? AIで変わる科学の方法

大上雅史

現代化学 = Chemistry today, (629) 28-30, Aug, 2023
Antisense oligonucleotide activity analysis based on opening and binding energies to targets

井澤和也, 井澤和也, 柳澤渓甫, 柳澤渓甫, 大上雅史, 大上雅史, 秋山泰, 秋山泰

情報処理学会研究報告(Web), 2021(MPS-134), 2021
Inhibitory Activity Model of Antisense Oligonucleotide Based on Estimation of Binding and Opening Energies to Target Sequences

井澤和也, 柳澤渓甫, 柳澤渓甫, 大上雅史, 大上雅史, 秋山泰, 秋山泰

情報処理学会研究報告(Web), 2021(BIO-65), 2021
構造情報に基づくタンパク質間相互作用の計算予測

大上雅史

ファインケミカル, 10月号 25-31, 2020
Improvement of homology search for metagenomic analysis by two-step seed search with reduced amino acid alphabet

高畠和輝, 伊澤和輝, 秋川元宏, 大上雅史, 秋山泰

情報処理学会研究報告(Web), 2020(BIO-61), 2020
Development of an efficient protein-ligand docking method by reuse of fragments

久保田陸人, 柳澤渓甫, 吉川寧, 大上雅史, 秋山泰

情報処理学会研究報告(Web), 2020(BIO-61), 2020
Megadock-Web: An Integrated Database of High-Throughput Structure-Based Protein-Protein Interaction Predictions

Masahito Ohue, Takanori Hayashi, Yuri Matsuzaki, Keisuke Yanagisawa, Yutaka Akiyama

BIOPHYSICAL JOURNAL, 116(3) 563A-563A, Feb, 2019
クローズアップ実験法 311 タンパク質間相互作用と複合体構造の予測結果を検索できるウェブサイト「MEGADOCK-Web」

大上雅史, 林孝紀, 秋山泰

実験医学, 37(9), 2019
Improvement of three-dimensional structure prediction method using interaction residue pair for multidomain proteins

松野駿平, 松野駿平, 大上雅史, 秋山泰

情報処理学会研究報告(Web), 2019(MPS-123), 2019
A Fast Protein-Protein Interaction Prediction Method with a Small Number of Representatives

林孝紀, 大上雅史, 秋山泰

情報処理学会研究報告(Web), 2019(BIO-57), 2019
タンパク質分子の柔軟性を考慮した新規ドッキングゲーム

飯野, 翼, 大上, 雅史, 秋山, 泰, 清水, 佳奈

第80回全国大会講演論文集, 2018(1) 931-932, Mar 13, 2018
Development of an efficient protein-ligand docking method for virtual screening by reuse of fragments

久保田陸人, 久保田陸人, 柳澤渓甫, 大上雅史, 秋山泰

情報処理学会研究報告(Web), 2018(MPS-118), 2018
Computational biostability prediction for cyclic peptides by multiple lasso solutions to construct interpretable prediction model

多治見隆志, 和久井直樹, 大上雅史, 秋山泰

情報処理学会研究報告(Web), 2018(MPS-118), 2018
クラウド上の分散GPU環境におけるタンパク質間相互作用予測計算フレームワークの開発

山本悠生, 大上雅史, 秋山泰

情報処理学会研究報告(Web), 2018(BIO-53), 2018
Development of MEGADOCK-Web-Mito: human mitochondrial predicted protein-protein interaction database

渡辺紘生, 渡辺紘生, 林孝紀, 大上雅史, 秋山泰

情報処理学会研究報告(Web), 2018(MPS-118), 2018
Oral metagenomic analysis using high-speed homology searching tool GHOSTX

117(110) 155-161, Jun 23, 2017
Human oral microbiota analysis toward the elucidation of periodontal disease factors

117(110) 149-154, Jun 23, 2017
Oral metagenomic analysis using high-speed homology searching tool GHOSTX

117(109) 209-215, Jun 23, 2017
Human oral microbiota analysis toward the elucidation of periodontal disease factors

117(109) 203-208, Jun 23, 2017
Cloud Computing for All-To-All Protein-Protein Docking on Azure HPC

Masahito Ohue, Yuki Yamamoto, Takanori Hayashi, Yuri Matsuzaki, Yutaka Akiyama

BIOPHYSICAL JOURNAL, 112(3) 451A-451A, Feb, 2017

Books and Other Publications

学振申請書の書き方とコツ第二版 : DC/PD獲得を目指す若者へ

大上, 雅史

講談社, Mar, 2021 (ISBN: 9784065231074)
学振申請書の書き方とコツ : DC/PD獲得を目指す若者へ

大上, 雅史

講談社, Apr, 2016 (ISBN: 9784061531604)
これだけ!生化学

生化学若い研究者の会, 稲垣, 賢二

秀和システム, Dec, 2014 (ISBN: 9784798042268)

Presentations

Highly precise protein-protein interaction prediction by integrating template-based and template-free protein docking

Masahito Ohue, Yuri Matsuzaki, Takehiro Shimoda, Takashi Ishida, Yutaka Akiyama

The 2013 Annual Conference of the Japanese Society for Bioinformatics (JSBi2013), Nov, 2013
The MEGADOCK project: Ultra-high-performance protein-protein interaction prediction tools on supercomputing environments

Takehiro Shimoda, Masahito Ohue, Yuri Matsuzaki, Takayuki Fujiwara, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama

ACM Conference on Bioinformatics, Computatioal Biology and Biomedical Informatics (ACM-BCB2013), Sep, 2013
MEGADOCK-GPU: Acceleration of Protein-Protein Docking Calculation on GPUs

Takehiro Shimoda, Takashi Ishida, Shuji Suzuki, Masahito Ohue, Yutaka Akiyama

ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2013 (ACM-BCB 2013), 2nd International Workshop on Parallel and Cloud-based Bioinformatics and Biomedicine (ParBio2013), Sep, 2013
Highly Precise Protein-Protein Interaction Prediction Based on Consensus Between Template-Based and de Novo Docking Methods

Masahito Ohue, Yuri Matsuzaki, Takehiro Shimoda, Takashi Ishida, Yutaka Akiyama

Great Lakes Bioinformatics Conference 2013, May, 2013
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 analyses

Masahito Ohue, Yuri Matsuzaki, Nobuyuki Uchikoga, Kohei Yamamoto, Takayuki Fujiwara, Takehiro Shimoda, Toshiyuki Sato, Takashi Ishida, Yutaka Akiyama

CAPRI 2013 5th Evaluation Meeting, Apr, 2013
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

大上雅史, 松崎由理, 石田貴士, 秋山泰

情報処理学会第32回バイオ情報学研究会, Dec, 2012
Improvement of the Protein-Protein Docking Prediction by Introducing a Simple Hydrophobic Interaction Model: an Application to Interaction Pathway Analysis

Masahito Ohue, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama

Pattern Recognition in Bioinformatics (PRIB2012), Nov, 2012
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

大上雅史, 石田貴士, 秋山泰

情報処理学会第29回バイオ情報学研究会, Jun, 2012
MEGADOCK: An all-to-all protein-protein interaction prediction system based on tertiary structures information

Masahito Ohue

IIT Madras-Tokyo Tech Joint Workshop on Bioinformatics and Large Scale Data Analysis, Jul, 2011 Invited
Development of a Protein-RNA Interaction Prediction Method Based on a Docking Calculation

Masahito Ohue, Yuri Matsuzaki, Yutaka Akiyama

The 2010 Annual Conference of the Japanese Society for Bioinformatics (JSBi2010), Dec, 2010
In silico prediction of PPI network with structure-based all-to-all docking

Masahito Ohue, Yuri Matsuzaki, Yusuke Matsuzaki, Toshiyuki Sato, Yutaka Akiyama

InCoB2010 - the 9th International Conference on Bioinformatics, Sep, 2010

Professional Memberships

Industrial Property Rights

特開2022-137148 情報処理装置、情報処理方法、情報処理プログラム、及び情報処理システム

秋山泰, 大上雅史, 柳澤渓甫, 吉川寧
特開2022-135688 予測装置、学習済みモデルの生成装置、予測方法、学習済みモデルの生成方法、予測プログラム、及び学習済みモデルの生成プログラム

秋山泰, 大上雅史, 柳澤渓甫, 吉川寧, 李佳男
特開2022-131959 予測装置、学習済みモデルの生成装置、予測方法、学習済みモデルの生成方法、予測プログラム、及び学習済みモデルの生成プログラム

秋山泰, 大上雅史, 柳澤渓甫, 吉川寧, 杉田昌岳, 藤江拓哉, 杉山聡, 村田翔太朗
特許第7125575号情報処理装置、情報処理方法、情報処理プログラム、及び情報処理システム

秋山泰, 大上雅史, 柳澤渓甫, 吉川寧
特開2022-078924 情報処理装置、情報処理方法、情報処理プログラム、及び情報処理システム

秋山泰, 大上雅史, 柳澤渓甫, 吉川寧
特許第7057004号予測装置、学習済みモデルの生成装置、予測方法、学習済みモデルの生成方法、予測プログラム、及び学習済みモデルの生成プログラム

秋山泰, 大上雅史, 柳澤渓甫, 吉川寧, 李佳男
特許第7057003号予測装置、学習済みモデルの生成装置、予測方法、学習済みモデルの生成方法、予測プログラム、及び学習済みモデルの生成プログラム

秋山泰, 大上雅史, 柳澤渓甫, 吉川寧, 杉田昌岳, 藤江拓哉, 杉山聡, 村田翔太朗

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Education

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Major Committee Memberships

Papers

Research Projects

Misc.

Books and Other Publications

Presentations

Professional Memberships

Industrial Property Rights

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