MITSUTAKE AYORI

Profile Information

Affiliation: Associate Professor, School of Science and Technology, Meiji University

Degree: 博士（理学）(The Graduate University for Advanced Studies)

J-GLOBAL ID: 200901014406191094
researchmap Member ID: 5000066241

Research Interests

Research Areas

Research History

Apr, 2018 - Present

Meiji University
Oct, 2013 - Mar, 2017

さきがけ研究者（併任）
Apr, 2012

大学専任講師
Apr, 2001 - Mar, 2012

Assistant Professor
Apr, 2006 - Mar, 2007

Sabbatical in Professor Charles L. Brooks,III Group, Department of Molecular Biology, The Scripps Research Institute
Apr, 2000 - Mar, 2001

日本学術振興会未来開拓学術研究推進事業 ,ﾘｻｰﾁｱｿｼｴｲﾄ
Oct, 1999 - Mar, 2000

日本学術振興会特別研究員（PD: DC2の残期間)
Apr, 1998 - Sep, 1999

日本学術振興会特別研究員(DC2)
Apr, 1997 - Sep, 1997

豊田工業大学非常勤講師
Senior Assistant Professor / Assistant Professor, Keio University Faculty of Science and Technology, Department of Physics

Committee Memberships

Jun, 2020 - Present

理事, 日本蛋白質科学会
Dec, 2018 - Present

幹事, 分子シミュレーション研究会
Jun, 2016 - Jun, 2019

理事（庶務）, 日本生物物理学会
Apr, 2013 - Mar, 2014

領域運営委員, 日本物理学会
Apr, 2009 - Mar, 2012

理事, 蛋白質科学会
Jan, 2010 - Dec, 2011

編集委員, 日本生物物理学会
Jan, 2010 - Dec, 2011

Editor, 日本生物物理学会
Apr, 2005 - Mar, 2007

理事, 蛋白質科学会
Apr, 2005 - Mar, 2007

Director, 蛋白質科学会

Awards

Papers

Structural and Computational Insights into Dynamics and Intermediate States of Orexin 2 Receptor Signaling.

Shun Yokoi, Ryoji Suno, Ayori Mitsutake

The journal of physical chemistry. B, May 9, 2024
Analysis of Protein Folding Simulation with Moving Root Mean Square Deviation.

Yutaka Maruyama, Ryo Igarashi, Yoshitaka Ushiku, Ayori Mitsutake

J. Chem. Inf. Model., 63(5) 1529-1541, Mar, 2023
Non-Markov-Type Analysis and Diffusion Map Analysis for Molecular Dynamics Trajectory of Chignolin at a High Temperature

Hiroshi Fujisaki, Hiromichi Suetani, Luca Maragliano, Ayori Mitsutake

Life, Aug 3, 2022
Computational Analysis of the SARS-CoV-2 RBD–ACE2-Binding Process Based on MD and the 3D-RISM Theory

Norio Yoshida, Yutaka Maruyama, Ayori Mitsutake, Akiyoshi Kuroda, Ryo Fujiki, Kodai Kanemaru, Daisuke Okamoto, Alexander E. Kobryn, Sergey Gusarov, Haruyuki Nakano

Journal of Chemical Information and Modeling, 62(11) 2889-2898, Jun 13, 2022
Structural Stability Analysis of Proteins Using End-to-End Distance: A 3D-RISM Approach

Yutaka Maruyama, Ayori Mitsutake

J, 5(1) 114-125, Feb 14, 2022
Molecular Dynamics Simulations for the Determination of the Characteristic Structural Differences between Inactive and Active States of Wild Type and Mutants of the Orexin2 Receptor.

Shun Yokoi, Ayori Mitsutake

The journal of physical chemistry. B, 125(17) 4286-4298, May 6, 2021
Universal Relation between Instantaneous Diffusivity and Radius of Gyration of Proteins in Aqueous Solution.

Eiji Yamamoto, Takuma Akimoto, Ayori Mitsutake, Ralf Metzler

Physical review letters, 126(12) 128101-128101, Mar 26, 2021
Mutation-induced change in chignolin stability from pi-turn to alpha-turn

Yutaka Maruyama, Shunpei Koroku, Misaki Imai, Koh Takeuchi, Ayori Mitsutake

RSC ADVANCES, 10(38) 22797-22808, Jun, 2020
Folding pathways of NuG2-a designed mutant of protein G-using relaxation mode analysis

Mitsutake Ayori, Takano Hiroshi

JOURNAL OF CHEMICAL PHYSICS, 151(4), Jul 28, 2019 Peer-reviewed
Identification of slow relaxation modes in a protein trimer via positive definite relaxation mode analysis

Karasawa Naoyuki, Mitsutake Ayori, Takano Hiroshi

JOURNAL OF CHEMICAL PHYSICS, 150(8), Feb 28, 2019 Peer-reviewed
Analysis of molecular dynamics simulations of 10-residue peptide, chignolin, using statistical mechanics: Relaxation mode analysis and three-dimensional reference interaction site model theory.

Yutaka Maruyama, Hiroshi Takano, Ayori Mitsutake

Biophysics and physicobiology, 16 407-429, 2019
Conformational change of a biomolecule studied by the weighted ensemble method: Use of the diffusion map method to extract reaction coordinates

Fujisaki Hiroshi, Moritsugu Kei, Mitsutake Ayori, Suetani Hiromichi

JOURNAL OF CHEMICAL PHYSICS, 149(13) 134112-134112, Oct 7, 2018 Peer-reviewed
Analysis of Structural Stability of Chignolin

Yutaka Maruyama, Ayori Mitsutake

Journal of Physical Chemistry B, 122(14) 3801-3814, Apr 12, 2018 Peer-reviewed
Relaxation mode analysis for molecular dynamics simulations of proteins

Ayori Mitsutake, Hiroshi Takano

Biophysical Reviews, 10(2) 375-389, Apr 1, 2018 Invited
Application of reference-modified density functional theory: Temperature and pressure dependences of solvation free energy

Tomonari Sumi, Yutaka Maruyama, Ayori Mitsutake, Kenji Mochizuki, Kenichiro Koga

JOURNAL OF COMPUTATIONAL CHEMISTRY, 39(4) 202-216, Feb, 2018 Peer-reviewed
Dynamical Analysis Methods for Protein Folding Simulations

Mitsutake Ayori, Takano Hiroshi

BIOPHYSICAL JOURNAL, 114(3) 45A, Feb, 2018
Two-step relaxation mode analysis with multiple evolution times applied to all-atom molecular dynamics protein simulation

N. Karasawa, A. Mitsutake, H. Takano

PHYSICAL REVIEW E, 96(6), Dec, 2017 Peer-reviewed
Stability of Unfolded and Folded Protein Structures Using a 3D-RISM with the RMDFT

Yutaka Maruyama, Ayori Mitsutake

JOURNAL OF PHYSICAL CHEMISTRY B, 121(42) 9881-9885, Oct, 2017 Peer-reviewed
Improved Relaxation Mode Analysis of a Hen Egg-White Lysozyme Protein

Naoyuki Karasawa, Ayori Mitsutake, Hiroshi Takano

BIOPHYSICAL JOURNAL, 112(3) 353A-353A, Feb, 2017
A reference-modified density functional theory: An application to solvation free-energy calculations for a Lennard-Jones solution

Tomonari Sumi, Yutaka Maruyama, Ayori Mitsutake, Kenichiro Koga

JOURNAL OF CHEMICAL PHYSICS, 144(22) 224104, Jun, 2016 Peer-reviewed

Misc.

Characteristic structural difference between inactive and active states of orexin 2 receptor determined using molecular dynamics simulations

Shun Yokoi, Ayori Mitsutake

Biophysical Reviews, 2021
How can we extract reaction coordinates from molecular dynamics simulations of biomolecules?

Fujisaki Hiroshi, Suetani Hiromichi, Mitsutake Ayori

Meeting Abstracts of the Physical Society of Japan, 72 3237-3237, 2017
19pBW-11 Rate calculations for conformational change of biomolecules using the milestoning method

Fujisaki Hiroshi, Mitsutake Ayori

Meeting Abstracts of the Physical Society of Japan, 71 3181-3181, 2016
Effective Sampling Algorithms and Analysis Methods for Molecular Simlations of Proteins

MITSUTAKE AYORI

日本物理学会学会誌, 70(3) 194-199, Mar, 2015 Peer-reviewedInvited
27pAB-11 Phase Transition of Water Confined in Slit Pores

Kaneko Toshihiro, Bai Jaeil, Yasuoka Kenji, Mitsutake Ayori, Zeng Xiao Cheng

Meeting abstracts of the Physical Society of Japan, 69(1) 397-397, Mar 5, 2014
30pAA-8 Relaxation mode analysis for small protein simulations

Mitsutake Ayori, Koizumi Yuta, Nagai Toshiki, Takano Hiroshi

Meeting abstracts of the Physical Society of Japan, 69(1) 437-437, Mar 5, 2014
30pAA-3 Molecular Dynamics SImulations of Equine Apomyoglobin at Low Temperatures

Suguri Sho, Mitsutake Ayori, Takano Hiroshi

Meeting abstracts of the Physical Society of Japan, 69(1) 436-436, Mar 5, 2014
学術賞受賞寄稿「多次元焼き戻し法の開発及び緩和モード解析とWHAM法の一般化による構造解析法の開発」

MITSUTAKE AYORI

分子シミュレーション研究会会誌"アンサンブル", 16(1) 1-6, Feb, 2014 Peer-reviewedInvited
27aXZC-6 Static and Dynamic Properties of Structural Fluctuations in Homologous Proteins

KOIZUMI Yuta, MITSUTAKE Ayori, TAKANO Hiroshi

Meeting abstracts of the Physical Society of Japan, 68(1) 433-433, Mar 26, 2013
27pXZD-3 Effective generalized-ensemble algorithms and analysis methods for biomolecular simulations

Mitsutake Ayori

Meeting abstracts of the Physical Society of Japan, 68(1) 437-437, Mar 26, 2013
20pAB-5 Relaxation Mode Analysis of Homologous Proteins

KOIZUMI Yuta, MITSUTAKE Ayori, TAKANO Hiroshi

Meeting abstracts of the Physical Society of Japan, 67(2) 337-337, Aug 24, 2012
27aPS-82 Generelized-ensemble simulations of small proteins

Mitsutake A., Sugita Y., Okamoto Y.

Meeting abstracts of the Physical Society of Japan, 57(1) 299-299, Mar 1, 2002
Generalized-ensemble simulations of Potts model systems

Nagasima Takehiro, Sugita Yuji, Mitsutake Ayori, Okamoto Yuko

Meeting abstracts of the Physical Society of Japan, 56(1) 228-228, Mar 9, 2001
Solvent Effects on Conformational Stability of Peptide and on Folding

F. Hirata, A. Mitsutake, M. Kinoshita, Y. Okamoto

Annual Conference on the Physical Chemistry of Liquids: Molecules - Macromolecules - Biomolecules，L54, 2000
“RISM理論を用いたMet-enkephalinのマルチカノニカルシミュレーション”

光武亜代理, 木下正弘, 岡本祐幸, 平田文男

１C1100，日本生物物理学会第38回年会予稿集(2000)., 2000
Simulated annealing study of α-helix forming tendency of a β-lactoglobulin fragment

Mitsutake A., Irisa M., Okamoto Y., Hirata F.

Biophysics, 38(2) S22, Sep 7, 1998
31a-P-4 Multicanonical study of the three-dimensional structures of a peptide with solvatoin free energy included a la extended scaled particle theory

Irisa M., Hansmann U., Mitsutake A., Okamoto Y., Hirata F.

Abstracts of the meeting of the Physical Society of Japan. Annual meeting, 51(3) 562-562, Mar 15, 1996
3a-G-8 Calculating the eigenvalues of large Hermitian matrices by second-order difference equations

Mitsutake A, Iitaka T., Okamoto Y.

Abstracts of the meeting of the Physical Society of Japan. Annual meeting, 51(4) 110-110, Mar 15, 1996

Books and Other Publications

Biomolecular Simulations: Methods and Protocols

A. Mitsutake, Y. Mori, Y. Okamoto (Role: Joint author)

2012

Presentations

リングポリマーブラシの静的・動的特性

川島聡, 高野宏, 光武亜代理

日本物理学会2017年年次大会, Mar 19, 2017, 日本物理学会
緩和モード解析による200残基程度の蛋白質のマイクロ秒程度の分子シミュレーションの動的解析

光武亜代理, 竹内恒, 高野宏

日本物理学会2017年年次大会, Mar 19, 2017, 日本物理学会
生体分子の分子シミュレーションから反応座標をどう抜き出すか？

藤崎弘士, 末谷大道, 光武亜代理

日本物理学会2017年年次大会, Mar 19, 2017, 日本物理学会
分子動力学法を用いたタンパク質の緩和モード解析II

唐澤直之, 光武亜代理, 高野宏

日本物理学会2017年年次大会, Mar 19, 2017, 日本物理学会
Improved Relaxation Mode Analysis of a Hen Egg-white Lysozyme Protein

KARASAWA NAOYUKI, MITSUTAKE AYORI, TAKANO HIROSHI

Biophysical Society 61st Annual Meeting, Feb 14, 2017
Investigating Dynamics and Kinetics of Proteins by using Relaxation Mode Analysis

MITSUTAKE AYORI

The Third Korean-Polish Conference on "Protein Folding: Theoretical and Experimental Approaches", Korea, Feb 8, 2017 Invited
Slow Relaxation Dynamics of Hen Egg-White Lysozyme Extracted by Relaxation Mode Analysis

"The Third Korean-Polish Conference on "Protein Folding: Theoretical and Experimental Approaches",Korea, Feb 6, 2017
Relaxation Mode Analysis for Molecular Simulations of Proteins

MITSUTAKE AYORI

JST-Bay Area Structural Biology Workshop, U.S., Jan 23, 2017 Invited
緩和モード解析を用いた蛋白質のダイナミクスの研究

光武亜代理, 高野宏

第30回分子シミュレーション討論会, Dec 1, 2016, 分子シミュレーション研究会
緩和モード解析による蛋白質系の遅い緩和ダイナミクスの抽出

唐澤直之, 光武亜代理, 高野宏

第30回分子シミュレーション討論会, Nov 30, 2016, 分子シミュレーション研究会
Dynamical analysis of protein simulations by using two-step relaxation mode analysis

KARASAWA NAOYUKI, MITUTAKE AYORI, TAKANO HIROSHI

The 54th Annual Meeting of the BSJ, Nov 26, 2016, 日本生物物理学会
Relaxation mode analysis for long time simulations of proteins

MITSUTAKE AYORI, TAKANO HIROSHI

The 54th Annual Meeting of the BSJ, Nov 26, 2016, 日本生物物理学会
分子動力学法を用いたタンパク質の緩和モード解析II

唐澤直之, 光武亜代理, 高野宏

日本物理学会2016年秋季大会, Sep 14, 2016, 日本物理学会
Two-step relaxation mode analysis with multiple evolution times of an all-atom molecular dynamics simulation of a protein

KARASAWA NAOYUKI, MITSUTAKE AYORI, TAKANO HIROSHI

International union of pure and applied physics 26th international conference on statistical physics, Jul 18, 2016
改良された緩和モード解析によるたんぱく質シミュレーションの動的解析

唐澤直之, 光武亜代理, 高野宏

第16回日本蛋白質科学会年会, Jun 9, 2016, 日本蛋白質科学会 Invited
緩和モード解析による蛋白質のダイナミクスの解析

光武亜代理, 高野宏

第16回日本蛋白質科学会年会, Jun 9, 2016, 日本蛋白質科学会
生体分子における構造変化遷移レートのマイルストーン法を用いた計算

FUJISAKI HIROSHI, MITSUTAKE AYORI

日本物理学会第71回年次大会2016年, Mar 19, 2016, 日本物理学会
分子動力を用いたタンパク質の緩和モード解析

KARASAWA NAOYUKI, MITSUTAKE AYORI, TAKANO HIROSHI

日本物理学会第71回年次大会2016年, Mar 19, 2016, 日本物理学会
Investigating kinetics of conformational change using molecular dynamics and milestoning

FUJISAKI HIROSHI, MITSUTAKE AYORI

Biophysical Society 60th Annual Meeting 2016, Mar 2, 2016, Biophysical Society
Relaxation mode analysis for protein simulations

MITSUTAKE AYORI, TAKANO HIROSHI

Biophysical Society 60th Annual Meeting 2016, Feb 29, 2016, Biophysical Society

Professional Memberships

Research Projects

Estimation of stability and functional changes due to amino acid substitution using molecular simulations

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (B), Japan Society for the Promotion of Science, Apr, 2020 - Mar, 2025
The mechanism of orexin receptors using molecular dynamics simulations

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), Japan Society for the Promotion of Science, Apr, 2022 - Mar, 2024
Novel characterization of rare events in dynamic data and its application to biological time series

Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C), Grant-in-Aid for Scientific Research (C), Japan Society for the Promotion of Science, Apr, 2016 - Mar, 2019

Fujisaki Hiroshi, Mitsutake Ayori, Moritsugu Kei, Matsunaga Yasuhiro
緩和モード解析によるタンパク質構造ダイナミクスの解明

Precursory Research for Embryonic Science and Technology, Oct, 2013 - Mar, 2017

光武亜代理
緩和モード解析による蛋白質の構造揺らぎの動的特徴

学事振興資金（個人研究特Ｂ）, 慶應義塾大学, Apr, 2013 - Mar, 2014

光武亜代理
多自由度・大規模系における反応と構造空間探索

Grant-in-Aid for Scientific Research, 新学術領域研究（研究領域提案型）「コンピュティクスによる物質デザイン：複合相関と非平衡ダイナミクス」, Sep, 2010 - Mar, 2014
多自由度・大規模系における反応と構造空間探索

Grant-in-Aid for Scientific Research, 新学術領域研究（研究領域提案型）「コンピュティクスによる物質デザイン：複合相関と非平衡ダイナミクス」, Sep, 2010 - Mar, 2014
物理化学的手法を用いた免疫系のペプチドの分子認識に対するシステムの構築

KLL指定研究プロジェクト, 2010 - 2011
拡張アンサンブル法による生体高分子系のシミュレーション

Grant-in-Aid for Scientific Research, Apr, 2007 - Mar, 2008
拡張アンサンブル法を用いた蛋白質の分子認識についてのシミュレーション手法の開発と応用

The Science Research Promotion Fund, Apr, 2006 - Mar, 2007
拡張アンサンブル法による蛋白質のフォールディングシミュレーション

Keio Gijuku Academic Development Funds, Apr, 2005 - Mar, 2006
拡張アンサンブル法によるタンパク質のフォールディングシミュレーション

Grant-in-Aid for Scientific Research, Apr, 2004 - Mar, 2006
生体高分子系の大規模な拡張アンサンブルシミュレーション

Keio Gijuku Academic Development Funds, Apr, 2004 - Mar, 2005
RISM理論で溶媒効果を取り入れた第一原理からのタンパク質の立体構造予測

Grant-in-Aid for Scientific Research, Apr, 2003 - Mar, 2005
拡張アンサンブルシミュレーションを用いた小タンパク質の巻き戻り問題の研究

Grant-in-Aid for Scientific Research, Apr, 2002 - Mar, 2005
生体高分子系の新しい拡張アンサンブル法の開発

Keio Gijuku Academic Development Funds, Apr, 2003 - Mar, 2004
拡張アンサンブル法を用いた大規模シミュレーションによる生体高分子の研究

Keio Gijuku Academic Development Funds, Apr, 2001 - Mar, 2002

Other

Organizing Committe (Vice Chair) of International Symposium on Extended Molecular Dynamics and Enhanced Sampling: Nosé Dynamics 30 Years (NOSE30)

Nov, 2014 - Nov, 2014

Profile Information

Research Interests

Research Areas

Research History

Committee Memberships

Awards

Papers

Misc.

Books and Other Publications

Presentations

Professional Memberships

Research Projects

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