Kobayashi Naoya 小林直也

… Alternative Names

KOBAYASHI Naoya 小林直也

Less

Researcher Number	60781945
Other IDs	https://orcid.org/0000-0002-6599-1680
Affiliation (Current)	2025: 奈良先端科学技術大学院大学, 先端科学技術研究科, 助教
Affiliation (based on the past Project Information) *help	2021 – 2024: 奈良先端科学技術大学院大学, 先端科学技術研究科, 助教 2018 – 2019: 大学共同利用機関法人自然科学研究機構(新分野創成センター、アストロバイオロジーセンター、生命創成探究, 生命創成探究センター, 特任研究員 2017: 分子科学研究所, 協奏分子システム研究センター, 特任研究員 2016: 信州大学, 繊維学部, アソシエイト研究員
Review Section/Research Field	Principal Investigator Transformative Research Areas, Section (II) / Basic Section 43040:Biophysics-related / Bio-related chemistry Except Principal Investigator Basic Section 37010:Bio-related chemistry / Medium-sized Section 43:Biology at molecular to cellular levels, and related fields / Basic Section 27040:Biofunction and bioprocess engineering-related
Keywords	Principal Investigator タンパク質デザイン / タンパク質複合体 / 計算機デザイン / 融合タンパク質 / ヘテロ複合体 / 相互作用面デザイン / タンパク質安定化 / オリゴマーデザイン / 酵素 / 超並列デザイン … More / ペプチドバーコーディング / 物性スクリーニング / 熱安定性解析 / 改変酵素 / オリゴマー構造 / 環境応答 / ダイナミクス解析 / 環境変化応答 / 自己組織化 / 蛋白質ナノブロック / 人工蛋白質 … More Except Principal Investigator タンパク質構造体 / タンパク質デザイン / 多量化 / 3Dドメインスワッピング / タンパク質 / クライオ電子顕微鏡 / ダイナミクス / 微生物型ロドプシン / 膜タンパク質 / タンパク質工学 / タンパク質複合体 / タンパク質ナノブロック / 人工タンパク質デザイン / レクチン Less

Development of a system for the design and creation of novel artificial lectin nanoblock complexes and their applications
- Principal Investigator
  
  新井亮一
- Project Period (FY)
  2024 – 2027
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 27040:Biofunction and bioprocess engineering-related
- Research Institution
  Shinshu University
異種タンパク質の自在な組合せを可能にするキメラタンパク質複合体のボトムアップ設計Principal Investigator
- Principal Investigator
  
  小林直也
- Project Period (FY)
  2024 – 2025
- Research Category
  
  Grant-in-Aid for Transformative Research Areas (A)
- Review Section
  
  Transformative Research Areas, Section (II)
- Research Institution
  Nara Institute of Science and Technology
二次構造モチーフに着目したデザイン戦略によるタンパク質複合体のボトムアップ構築Principal Investigator
- Principal Investigator
  
  小林直也
- Project Period (FY)
  2022 – 2023
- Research Category
  
  Grant-in-Aid for Transformative Research Areas (A)
- Review Section
  
  Transformative Research Areas, Section (II)
- Research Institution
  Nara Institute of Science and Technology
The analysis of structural dynamics of microbial rhodopsins
- Principal Investigator
  
  加藤英明
- Project Period (FY)
  2022 – 2026
- Research Category
  
  Grant-in-Aid for Scientific Research (A)
- Review Section
  
  Medium-sized Section 43:Biology at molecular to cellular levels, and related fields
- Research Institution
  The University of Tokyo
Comprehensive understanding and application of protein 3D domain swapping
- Principal Investigator
  
  廣田俊
- Project Period (FY)
  2021 – 2024
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 37010:Bio-related chemistry
- Research Institution
  Nara Institute of Science and Technology
Computational design and thermal stability analysis of oligomeric proteinsPrincipal Investigator
- Principal Investigator
  
  Kobayashi Naoya
- Project Period (FY)
  2018 – 2019
- Research Category
  
  Grant-in-Aid for Early-Career Scientists
- Review Section
  
  Basic Section 43040:Biophysics-related
- Research Institution
  Center for Novel Science Initatives, National Institutes of Natural Sciences
Structural transition of de novo proteins and reconstruction of protein nanobuilding block complexes.Principal Investigator
- Principal Investigator
  
  KOBAYASHI Naoya
- Project Period (FY)
  2016 – 2017
- Research Category
  
  Grant-in-Aid for Research Activity Start-up
- Research Field
  
  Bio-related chemistry
- Research Institution
  Institute for Molecular Science
  Shinshu University

All 2024 2023 2022 2020 2019 2018 2017 2016

All Journal Article Presentation Patent

[Journal Article] タンパク質と他分子の複合体構造を予測するAI・生成するAI2024
- Author(s)
  小林　直也
- Volume
  42
- Pages
  436
- DOI
  10.18958/7407-00004-0001154-00
- Language
  Japanese
- Data Source
  KAKENHI-PUBLICLY-22H05426
[Journal Article] AlphaFold時代の生成モデルが身近にするタンパク質設計2023
- Author(s)
  小林　直也, 佐久間　航也
- Volume
  41
- Pages
  2601
- DOI
  10.18958/7335-00001-0000603-00
- Language
  Japanese
- Data Source
  KAKENHI-PUBLICLY-22H05426
[Journal Article] Protein Cages and Nanostructures Constructed from Protein Nanobuilding Blocks2023
- Author(s)
  Kobayashi Naoya、Arai Ryoichi
- Journal Title
  
  Methods in Molecular Biology
  
  Volume: 2671 Pages: 79-94
- DOI
  10.1007/978-1-0716-3222-2_4
- ISBN
  9781071632215, 9781071632222
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17KK0104, KAKENHI-PUBLICLY-22H05426
[Journal Article] 標的タンパク質の構造情報のみから結合タンパク質の設計が可能になった2022
- Author(s)
  小林直也
- Journal Title
  
  Farumashia
  
  Volume: 58 Issue: 12 Pages: 1159-1159
- DOI
  10.14894/faruawpsj.58.12_1159
- ISSN
  0014-8601, 2189-7026
- Language
  Japanese
- Data Source
  KAKENHI-PUBLICLY-22H05426
[Journal Article] Design of artificial protein complexes of protein nano-building blocks2019
- Author(s)
  小林直也、川上了史、新井亮一
- Journal Title
  
  生化学
  
  Volume: 91 Issue: 2 Pages: 255-259
- DOI
  10.14952/SEIKAGAKU.2019.910255
- NAID
  40021942521
- ISSN
  0037-1017
- Year and Date
  2019-04-25
- Language
  Japanese
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16K05841, KAKENHI-PROJECT-18K05324, KAKENHI-PROJECT-17KK0104, KAKENHI-PROJECT-19H02522, KAKENHI-PROJECT-18K14668
[Journal Article] Self-assembling Supramolecular Complex Nanostructures Constructed from <i>de Novo</i> Protein Nanobuilding Blocks2018
- Author(s)
  小林直也、新井亮一
- Journal Title
  
  Seibutsu Butsuri
  
  Volume: 58 Issue: 6 Pages: 313-315
- DOI
  10.2142/biophys.58.313
- NAID
  130007521690
- ISSN
  0582-4052, 1347-4219
- Language
  Japanese
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16K05841, KAKENHI-PROJECT-18K14668
[Journal Article] Self-Assembling Supramolecular Nanostructures Constructed from de Novo Extender Protein Nanobuilding Blocks2018
- Author(s)
  Kobayashi Naoya、Inano Kouichi、Sasahara Kenji、Sato Takaaki、Miyazawa Keisuke、Fukuma Takeshi、Hecht Michael H、Song Chihong、Murata Kazuyoshi、Arai Ryoichi
- Journal Title
  
  ACS Synthetic Biology
  
  Volume: 7 Issue: 5 Pages: 1381-1394
- DOI
  10.1021/acssynbio.8b00007
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16K05841, KAKENHI-PUBLICLY-16H00761, KAKENHI-PROJECT-16H06837, KAKENHI-PROJECT-18K14668, KAKENHI-PROJECT-16H02111, KAKENHI-PROJECT-16J01938
[Journal Article] Design and construction of self-assembling supramolecular protein complexes using artificial and fusion proteins as nanoscale building blocks2017
- Author(s)
  Naoya Kobayashi, Ryoichi Arai
- Journal Title
  
  Current Opinion in Biotechnology
  
  Volume: 46 Pages: 57-65
- DOI
  10.1016/j.copbio.2017.01.001
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PUBLICLY-16H00761, KAKENHI-PROJECT-16H06837, KAKENHI-PROJECT-16K05841
[Journal Article] 二量体形成新規人工タンパク質を用いたタンパク質ナノブロック開発による自己組織化ナノ構造複合体の創製2016
- Author(s)
  小林直也，新井亮一
- Journal Title
  
  分子研レターズ
  
  Volume: 73 Pages: 30-31
- Open Access
- Data Source
  KAKENHI-PROJECT-16H06837
[Journal Article] バイナリーパターン配列デザインによるデノボ蛋白質の創出と蛋白質ナノブロックによる超分子複合体の創生2016
- Author(s)
  小林直也，木村尚弥，新井亮一
- Journal Title
  
  生物工学会誌
  
  Volume: 94 Pages: 485-488
- Open Access
- Data Source
  KAKENHI-PROJECT-16H06837
[Journal Article] 人工蛋白質で「かたち」をつくろう―ブロック遊びしようよ！―2016
- Author(s)
  小林直也，新井亮一
- Journal Title
  
  生物工学会誌
  
  Volume: 94 Pages: 270-270
- Open Access
- Data Source
  KAKENHI-PROJECT-16H06837
[Patent] 耐熱性βグルコシダーゼ2018
- Inventor(s)
  古賀信康, 小林直也, 南慎太朗
- Industrial Property Rights Holder
  自然科学研究機構
- Industrial Property Rights Type
  特許
- Industrial Property Number
  2018-172810
- Filing Date
  2018
- Data Source
  KAKENHI-PROJECT-18K14668
[Presentation] 局所構造に着目したオリゴマーデザインとモノマー新規フォールドの手編み設計2023
- Author(s)
  小林直也
- Organizer
  計算タンパク質科学研究会
- Data Source
  KAKENHI-PUBLICLY-22H05426
[Presentation] e novo design of new protein folds and heterooligomeric proteins by intuitive and simple methods2023
- Author(s)
  Naoya Kobayashi
- Organizer
  日本進化学会第25回大会
- Invited
- Data Source
  KAKENHI-PUBLICLY-22H05426
[Presentation] Combinatorial design of heterooligomeric proteins by recombination of structural domains through sterically analogous structure motifs2023
- Author(s)
  Marino Yamamoto, Naoya Kobayashi, Shun Hirota
- Organizer
  第61回日本生物物理学会年会
- Data Source
  KAKENHI-PUBLICLY-22H05426
[Presentation] 配列デザインと立体構造予測の繰り返しによる手編みタンパク質構造の高品質化2023
- Author(s)
  小林直也, 廣田俊, 佐久間航也
- Organizer
  第23回日本蛋白質科学会年会
- Data Source
  KAKENHI-PUBLICLY-22H05426
[Presentation] Construction of stable c-type cytochrome dimers utilizing computational design inspired by 3D domain swapping.2023
- Author(s)
  Naoya Kobayashi, Yuma Yoshida, Hideaki Ogata, Tsuyoshi Mashima, Shun Hirota
- Organizer
  第61回日本生物物理学会年会
- Data Source
  KAKENHI-PUBLICLY-22H05426
[Presentation] ヘリックス-ループ-ヘリックスモチーフのヘリックス-ヘリックス角に着目したタンパク質複合体構造の計算機デザイン2022
- Author(s)
  山本麻里乃, 小林直也, 廣田俊
- Organizer
  第60回日本生物物理学会年会
- Data Source
  KAKENHI-PUBLICLY-22H05426
[Presentation] 耐熱性シトクロムcのドメインスワッピング2量体構造の計算機デザイン2022
- Author(s)
  吉田悠真, 小林直也, 真島剛史, 廣田俊
- Organizer
  第22回蛋白質科学会年会
- Data Source
  KAKENHI-PUBLICLY-22H05426
[Presentation] 気軽に試せる計算機タンパク質デザインに向けて2022
- Author(s)
  小林直也, 廣田俊
- Organizer
  第60回日本生物物理学会年会
- Data Source
  KAKENHI-PUBLICLY-22H05426
[Presentation] 二次構造モチーフに着目したドメインスワッピング構造の計算機デザインによるタンパク質複合体の構築2022
- Author(s)
  小林直也, 吉田悠真, 真島剛史, 廣田俊
- Organizer
  第22回蛋白質科学会年会
- Data Source
  KAKENHI-PUBLICLY-22H05426
[Presentation] Toward creation of artificial proteins self-assembling into diverse symmetric structures: computational design and experimental screening2020
- Author(s)
  Naoya Kobayashi, Nobuyasu Koga
- Organizer
  The 1st International Symposium on Molecular Engine
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18K14668
[Presentation] Toward design of thermostable beta-glucosidase with structure-based sequence profile2018
- Author(s)
  Kobayashi, N., Minami, S., Uchiyama, T., Sunagawa, N., Igarashi, K., and Koga, N.
- Organizer
  International Symposium on "Artificial Cell Reactor Science and Technology" (Tokyo)
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18K14668
[Presentation] 立体構造に基づく配列プロファイルを利用したβ-グルコシダーゼの熱安定化2018
- Author(s)
  小林直也, 南慎太朗, 小杉貴洋, 内山拓, 砂川直輝, 五十嵐圭日子, 野地博行, 古賀信康
- Organizer
  最終成果報告会―人工細胞リアクタが拓くイノベーション―(東京)
- Data Source
  KAKENHI-PROJECT-18K14668
[Presentation] Toward design of thermostable beta-glucosidase with structure-based sequence profile2018
- Author(s)
  Kobayashi, N., Minami, S., Uchiyama, T., Sunagawa, N., Igarashi, K., Noji, H., and Koga, N.
- Organizer
  第56回日本生物物理学会年会 (岡山)
- Data Source
  KAKENHI-PROJECT-18K14668
[Presentation] 多様なタンパク質複合体構造の合理デザインに向けて2018
- Author(s)
  小林直也, 古賀信康
- Organizer
  第18回日本蛋白質科学会年会(新潟)
- Data Source
  KAKENHI-PROJECT-18K14668
[Presentation] Cumulative thermostabilization of beta-glucosidase with structure-based sequence profile information2018
- Author(s)
  Kobayashi, N.
- Organizer
  分子研研究会「New Frontier in Protein Design & Engineering」(愛知)
- Data Source
  KAKENHI-PROJECT-18K14668
[Presentation] pH-dependent structural transition of self-assembling nanostructures constructed from protein nanobuilding blocks using a dimeric de novo protein2017
- Author(s)
  Naoya Kobayashi, Takuya Sengoku, Takaaki Sato, Ryoichi Arai
- Organizer
  Okazaki Conference 2017 on Grand Challenges in Small-angle Scattering
- Place of Presentation
  岡崎コンファレンスセンター(愛知県岡崎市)
- Year and Date
  2017-03-18
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16H06837
[Presentation] pH-dependent structural transition of a dimeric de novo protein WA20 and reconstruction of protein nanobuilding block complexes2017
- Author(s)
  Naoya Kobayashi, Takuya Sengoku, Takaaki Sato, Ryoichi Arai
- Organizer
  第17回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-16H06837
[Presentation] タンパク質ナノブロックによる動的秩序構造形成2017
- Author(s)
  木村尚弥、小林直也、新井亮一
- Organizer
  日本化学会第97春季年会
- Place of Presentation
  慶應義塾大学日吉キャンパス(神奈川県横浜市)
- Year and Date
  2017-03-16
- Invited
- Data Source
  KAKENHI-PROJECT-16H06837
[Presentation] Dynamical Ordering Nanostructures Constructed from Protein Nanobuilding Blocks2017
- Author(s)
  Naoya Kimura, Naoya Kobayashi, Ryoichi Arai
- Organizer
  The 5th International Symposium of Dynamical Ordering of Biomolecular Systems for Creation of Integrated Functions
- Place of Presentation
  東京大学(東京都目黒区)
- Year and Date
  2017-01-21
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16H06837
[Presentation] Self-assembling supramolecular nanostructures created from de novo protein nanobuilding blocks2017
- Author(s)
  Naoya Kimura, Naoya Kobayashi, Ryoichi Arai
- Organizer
  Okazaki Conference 2017 on Grand Challenges in Small-angle Scattering, Okazaki
- Place of Presentation
  岡崎コンファレンスセンター(愛知県岡崎市)
- Year and Date
  2017-03-18
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16H06837
[Presentation] 人工タンパク質をブロックに見立てた超分子ナノ構造複合体の設計構築2016
- Author(s)
  小林直也、木村尚弥、新井亮一
- Organizer
  第54回日本生物物理学会年会
- Place of Presentation
  つくば国際会議場(茨城県つくば市)
- Year and Date
  2016-11-25
- Invited
- Data Source
  KAKENHI-PROJECT-16H06837
[Presentation] Self-assembling supramolecular nano-architectures created from de novo protein nano-building blocks2016
- Author(s)
  Naoya Kimura, Naoya Kobayashi, Ryoichi Arai
- Organizer
  第68回日本生物工学会大会
- Place of Presentation
  富山国際会議場・ANAクラウンプラザホテル(富山県富山市)
- Year and Date
  2016-09-28
- Invited
- Data Source
  KAKENHI-PROJECT-16H06837
[Presentation] De Novo Protein Nano-Building Block Approach for “Synthetic Structural Biology” to Create Artificial Supramolecular Protein Complexes2016
- Author(s)
  Ryoichi Arai, Naoya Kimura, Naoya Kobayashi, Michael H. Hecht
- Organizer
  THE 42nd NAITO CONFERENCE ON In the Vanguard of Structural Biology: Revolutionizing Life Sciences
- Place of Presentation
  シャトレーゼガトーキングダムサッポロ(北海道札幌市)
- Year and Date
  2016-10-04
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16H06837
[Presentation] 人工蛋白質ナノブロックによる多様な自己組織化超分子ナノ構造複合体：ネオバイオ超分子の創生を目指して2016
- Author(s)
  小林直也、木村尚弥、新井亮一
- Organizer
  第39回日本分子生物学会年会
- Place of Presentation
  パシフィコ横浜(神奈川県横浜市)
- Year and Date
  2016-11-30
- Invited
- Data Source
  KAKENHI-PROJECT-16H06837
[Presentation] 蛋白質ナノブロック用超安定化人工蛋白質SUWA (Super WA20)の特性解析及び構造解析2016
- Author(s)
  木村尚弥、小林直也、新井亮一
- Organizer
  第68回日本生物工学会大会
- Place of Presentation
  富山国際会議場・ANAクラウンプラザホテル(富山県富山市)
- Year and Date
  2016-09-28
- Data Source
  KAKENHI-PROJECT-16H06837

1. 新井亮一 (50344023)

# of Collaborated Projects: 1 results

# of Collaborated Products: 3 results
2. 舘野浩章 (30450670)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
3. 川上了史 (60566800)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
4. 加藤英明 (80805961)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
5. 井上圭一 (90467001)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
6. 廣田俊 (90283457)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results

Kobayashi Naoya 小林 直也

KOBAYASHI Naoya 小林 直也

Research Projects

Research Products

Co-Researchers

Development of a system for the design and creation of novel artificial lectin nanoblock complexes and their applications

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

異種タンパク質の自在な組合せを可能にするキメラタンパク質複合体のボトムアップ設計Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

二次構造モチーフに着目したデザイン戦略によるタンパク質複合体のボトムアップ構築Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

The analysis of structural dynamics of microbial rhodopsins

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Comprehensive understanding and application of protein 3D domain swapping

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Computational design and thermal stability analysis of oligomeric proteinsPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Structural transition of de novo proteins and reconstruction of protein nanobuilding block complexes.Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

[Journal Article] タンパク質と他分子の複合体構造を予測するAI・生成するAI2024

Author(s)

Volume

Pages

DOI

Language

Data Source

[Journal Article] AlphaFold時代の生成モデルが身近にするタンパク質設計2023

Author(s)

Volume

Pages

DOI

Language

Data Source

[Journal Article] Protein Cages and Nanostructures Constructed from Protein Nanobuilding Blocks2023

Author(s)

Journal Title

DOI

ISBN

Data Source

[Journal Article] 標的タンパク質の構造情報のみから結合タンパク質の設計が可能になった2022

Author(s)

Journal Title

DOI

ISSN

Language

Data Source

[Journal Article] Design of artificial protein complexes of protein nano-building blocks2019

Author(s)

Journal Title

DOI

NAID

ISSN

Kobayashi Naoya 小林直也

KOBAYASHI Naoya 小林直也