Chiba Shuntaro - My portal

Profile Information

J-GLOBAL ID: 201901001822662988
researchmap Member ID: B000381233

Research Areas

Life sciences / Biophysics /

Papers

Enhanced Coarse-Grained Molecular Dynamics Simulation with a Smoothed Hybrid Potential Using a Neural Network Model

Ryo Kanada, Atsushi Tokuhisa, Yusuke Nagasaka, Shingo Okuno, Koichiro Amemiya, Shuntaro Chiba, Gert-Jan Bekker, Narutoshi Kamiya, Koichiro Kato, Yasushi Okuno

Journal of Chemical Theory and Computation, Jan 9, 2024
Ensemble-Learning and Feature Selection Techniques for Enhanced Antisense Oligonucleotide Efficacy Prediction in Exon Skipping.

Alex Zhu, Shuntaro Chiba, Yuki Shimizu, Katsuhiko Kunitake, Yasushi Okuno, Yoshitsugu Aoki, Toshifumi Yokota

Pharmaceutics, 15(7), Jun 24, 2023 Peer-reviewed
eSkip-Finder: a machine learning-based web application and database to identify the optimal sequences of antisense oligonucleotides for exon skipping

Shuntaro Chiba, Kenji Rowel Q Lim, Narin Sheri, Saeed Anwar, Esra Erkut, Md Nur Ahad Shah, Tejal Aslesh, Stanley Woo, Omar Sheikh, Rika Maruyama …

Nucleic Acids Research, 49(W1) W193-W198, Jun 9, 2021 Peer-reviewedLead author
Structure-based design and discovery of novel anti-tissue factor antibodies with cooperative double-point mutations, using interaction analysis

Shuntaro Chiba, Aki Tanabe, Makoto Nakakido, Yasushi Okuno, Kouhei Tsumoto, Masateru Ohta

Scientific Reports, 10(1) 17590-17590, Dec, 2020 Peer-reviewedLead author
Coarse-Grained Diffraction Template Matching Model to Retrieve Multiconformational Models for Biomolecule Structures from Noisy Diffraction Patterns

Atsushi Tokuhisa, Ryo Kanada, Shuntaro Chiba, Kei Terayama, Yuta Isaka, Biao Ma, Narutoshi Kamiya, Yasushi Okuno

Journal of Chemical Information and Modeling, 60(6) 2803-2818, Jun 22, 2020 Peer-reviewed
Improvement in predicting drug sensitivity changes associated with protein mutations using a molecular dynamics based alchemical mutation method.

Fumie Ono, Shuntaro Chiba, Yuta Isaka, Shigeyuki Matsumoto, Biao Ma, Ryohei Katayama, Mitsugu Araki, Yasushi Okuno

Scientific reports, 10(1) 2161-2161, Feb 7, 2020 Peer-reviewed
Stabilization Mechanism for a Nonfibrillar Amyloid β Oligomer Based on Formation of a Hydrophobic Core Determined by Dissipative Particle Dynamics

Ryoko Kawai, Shuntaro Chiba, Koji Okuwaki, Ryo Kanada, Hideo Doi, Masahiro Ono, Yuji Mochizuki, Yasushi Okuno

ACS Chemical Neuroscience, 11(3) 385-394, Feb 5, 2020 Peer-reviewed
A prospective compound screening contest identified broader inhibitors for Sirtuin 1

Shuntaro Chiba, Masahito Ohue, Anastasiia Gryniukova, Petro Borysko, Sergey Zozulya, Nobuaki Yasuo, Ryunosuke Yoshino, Kazuyoshi Ikeda, Woong-Hee Shin, Daisuke Kihara …

Scientific Reports, 9(1) 19585, Dec, 2019 Peer-reviewed
Force-field parametrization based on radial and energy distribution functions

Shuntaro Chiba, Yasushi Okuno, Teruki Honma, Mitsunori Ikeguchi

Journal of Computational Chemistry, 40(29) 2577-2585, Nov, 2019 Peer-reviewed
An iterative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes

Shuntaro Chiba, Takashi Ishida, Kazuyoshi Ikeda, Masahiro Mochizuki, Reiji Teramoto, Y-h. Taguchi, Mitsuo Iwadate, Hideaki Umeyama, Chandrasekaran Ramakrishnan, A. Mary Thangakani …

SCIENTIFIC REPORTS, 7, Sep, 2017 Peer-reviewed
Kirkwood-Buff Integrals for Aqueous Urea Solutions Based upon the Quantum Chemical Electrostatic Potential and Interaction Energies

Shuntaro Chiba, Tadaomi Furuta, Seishi Shimizu

JOURNAL OF PHYSICAL CHEMISTRY B, 120(31) 7714-7723, Aug, 2016 Peer-reviewed
Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target

Shuntaro Chiba, Kazuyoshi Ikeda, Takashi Ishida, M. Michael Gromiha, Y-h. Taguchi, Mitsuo Iwadate, Hideaki Umeyama, Kun-Yi Hsin, Hiroaki Kitano, Kazuki Yamamoto …

SCIENTIFIC REPORTS, 5, Nov, 2015 Peer-reviewed
ATP-Induced Conformational Changes of Nucleotide-Binding Domains in an ABC Transporter. Importance of the Water-Mediated Entropic Force

Tomohiko Hayashi, Shuntaro Chiba, Yusuke Kaneta, Tadaomi Furuta, Minoru Sakurai

JOURNAL OF PHYSICAL CHEMISTRY B, 118(44) 12612-12620, Nov, 2014 Peer-reviewed
Water-mediated forces between the nucleotide binding domains generate the power stroke in an ABC transporter

Tomoka Furukawa-Hagiya, Norio Yoshida, Shuntaro Chiba, Tomohiko Hayashi, Tadaomi Furuta, Yoshiro Sohma, Minoru Sakurai

CHEMICAL PHYSICS LETTERS, 616 165-170, Nov, 2014 Peer-reviewed
A Morphometric Approach for the Accurate Solvation Thermodynamics of Proteins and Ligands

Yuichi Harano, Roland Roth, Shuntaro Chiba

JOURNAL OF COMPUTATIONAL CHEMISTRY, 34(23) 1969-1974, Sep, 2013 Peer-reviewed
Dynamics and structural changes induced by ATP and/or substrate binding in the inward-facing conformation state of P-glycoprotein

Yurika Watanabe, Wei-Lin Hsu, Shuntaro Chiba, Tomohiko Hayashi, Tadaomi Furuta, Minoru Sakurai

CHEMICAL PHYSICS LETTERS, 557 145-149, Feb, 2013 Peer-reviewed
1P041 Theoretical analyses of the nucleotide-binding domain dimerization of ABC transporters: roles of ATP and water(01B. Protein:Structure & Function,Poster)

Hayashi Tomohiko, Furukawa-Hagiya Tomoka, Chiba Shuntaro, Furuta Tadaomi, Yoshida Norio, Sakurai Minoru

Seibutsu Butsuri, 53(1) S112, 2013
The Power Stroke Driven by ATP Binding in CFTR As Studied by Molecular Dynamics Simulations

Tomoka Furukawa-Hagiya, Tadaomi Furuta, Shuntaro Chiba, Yoshiro Sohma, Minoru Sakurai

JOURNAL OF PHYSICAL CHEMISTRY B, 117(1) 83-93, Jan, 2013 Peer-reviewed
Evaluation of protein-ligand binding free energy focused on its entropic components

Shuntaro Chiba, Yuich Harano, Roland Roth, Masahiro Kinoshita, Minoru Sakurai

JOURNAL OF COMPUTATIONAL CHEMISTRY, 33(5) 550-560, Feb, 2012 Peer-reviewed
3PT133 ATP-Binding induced conformational change in CFTR as studied by MD simulation(The 50th Annual Meeting of the Biophysical Society of Japan)

Hagiya Tomoka, Furuta Tadaomi, Chiba Shuntaro, Sohma Yoshiro, Sakurai Minoru

Seibutsu Butsuri, 52 S163, 2012

Awards

Dec, 2020

SAR Presentation Award
2019

構造活性相関シンポジウム優秀発表賞（口頭）, 抗原・抗体複合体立体構造に基づく２アミノ酸同時変異戦略による新規抗体創製, 第47回構造活性相関シンポジウム

千葉峻太朗, 大田雅照, 田部亜季, 中木戸誠, 津本浩平, 奥野恭史
2014

The Best Poster Presentation Award

Misc.

Structure-Based Affinity Maturation of Antibody Based on Double-Point Mutations

Shuntaro Chiba, Yasushi Okuno, Masateru Ohta

Computer-Aided Antibody Design, 323-331, Nov 9, 2022 Lead author
製剤処方設計AIの開発

岩田浩明, 千葉峻太朗, 長谷川亜樹, 大田雅照, 奥野恭史

2022
【構造生命科学による創薬への挑戦】計算機から創薬へ協調的2アミノ酸残基同時変異体の相互作用解析による新規抗体のStructure-Based Design

千葉峻太朗, 大田雅照

医学のあゆみ, 278(6) 663-669, Aug, 2021
動径分布関数・エネルギー分布関数をもとにした粗視化力場パラメータ決定手法の改良

千葉峻太朗, 奥野恭史, 奥野恭史, 本間光貴, 池口満徳, 池口満徳

分子シミュレーション討論会講演要旨集, 33rd, 2019
散逸動力学シミュレーションによるアミロイドβオリゴマーの自己組織化の検討

河合良子, 千葉峻太朗, 金田亮, 奥脇弘次, 土居英男, 望月祐志, 望月祐志, 奥野恭史, 奥野恭史, 奥野恭史

日本細胞生物学会大会(Web), 71st, 2019
散逸動力学シミュレーションによるアミロイドβオリゴマーの自己組織化の検討

河合良子, 千葉峻太朗, 金田亮, 奥脇弘次, 土居英男, 望月祐志, 望月祐志, 奥野恭史, 奥野恭史

日本コンピュータ化学会年会講演予稿集, 2019, 2019
動径分布関数・エネルギー分布関数をもとにした進化戦略による力場パラメータ決定手法

千葉峻太朗, 池口満徳, 奥野恭史

分子シミュレーション討論会講演要旨集, 32nd 92, Nov 28, 2018
Computer-aided Drug Discovery Based on Big Data Analysis and Molecular Simulation

千葉峻太朗, 荒木望嗣, 奥野恭史

シミュレーション = Journal of the Japan Society for Simulation Technology, 37(1) 42-49, Mar, 2018
FMO法を用いた抗dengue virus薬の創薬標的蛋白質と既知化合物間の相互作用解析

吉野龍ノ介, 安尾信明, 千葉峻太朗, 萩原陽介, 大野一樹, 折田正弥, 関嶋政和, 関嶋政和, 関嶋政和

日本熱帯医学会大会プログラム抄録集, 54th, 2013
Evaluation of protein-ligand binding free energy focused on its entropic components (vol 33, pg 550, 2012)

Shuntaro Chiba, Yuichi Harano, Roland Roth, Masahiro Kinoshita, Minoru Sakurai

JOURNAL OF COMPUTATIONAL CHEMISTRY, 33(27) 2210-2210, Oct, 2012
リガンド－タンパク質間の結合自由エネルギーに対するマルチフィジックス的計算手法の比較および評価

千葉峻太郎, 野村淳磨, 原野雄一, 木下正弘, 櫻井実

第46回日本生物物理学会年会，福岡国際会議場，2008.12.3-5, 2008

Presentations

新規モダリティ創薬に資する次世代計算手法の開発

千葉峻太朗

創薬モダリティ基盤研究会講演会（（一財）バイオインダストリー協会）, Apr 8, 2024 Invited
「富岳」を活用した創薬DX プラットフォーム－標的遺伝子探索とリード化合物創出

千葉峻太朗

第448回CBI学会講演会, Aug 21, 2023 Invited
KBI derived from MD simulations using a polarizable force field

Shuntaro Chiba

May 20, 2019 Invited

Teaching Experience

分子シミュレーション演習 (東京工業大学大学院)

Research Projects

Simulation- and AI-driven next-generation medicine and drug discovery based on "Fugaku"

Program for Promoting Researches on the Supercomputer Fugaku", MEXT, Apr, 2023 - Mar, 2026
抗体デザインのための協同的に働く多アミノ酸変異による親和性・物性の多目的最適化

科学研究費助成事業基盤研究(C), 基盤研究(C), 日本学術振興会, Apr, 2022 - Mar, 2025

千葉峻太朗

Social Activities

スパコンで計算してみた（ウイルスの変異が薬剤分子の振る舞いにどう影響するのか）

Guest, Planner, Performer

国立研究開発法人理化学研究所横浜キャンパス・公立大学法人横浜市立大学鶴見キャンパス, 理化学研究所横浜市立大学一般公開 on the Web, YOUTUBE, Oct 10, 2020 - Present