Database Development and Functional Analysis of Protein Disorder Regions

• Project/Area Number: 20500269
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Bioinformatics/Life informatics
• Research Institution: The University of Tokyo
• Principal Investigator: SHIMIZU Kentaro The University of Tokyo, 大学院・農学生命科学研究科, 教授 (80178970)
• Co-Investigator(Kenkyū-buntansha): 中村 周吾 東京大学, 大学院・農学生命科学研究科, 准教授 (90272442)
• Project Period (FY): 2008 – 2010
• Project Status: Completed (Fiscal Year 2010)
• Budget Amount: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000); Fiscal Year 2010: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000); Fiscal Year 2009: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000); Fiscal Year 2008: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
• Keywords: プロテオーム / 生体生命情報学 / タンパク質 / 不規則領域 / 蛋白質 / 構造予測 / 構造評価 / 構造精密化 / ブロテオーム

Research Abstract

We developed a new method for defining the degree of disorder of protein structures. The results of this analysis were stored in our protein disorder database. We also analyzed the relation between the disorder regions and functional sites of proteins.

Research Products

• [Journal Article] Protein-Protein Docking Using Multi-layered Spherical Basis Functions (2011)
  • Author(s): K.Sumikoshi, T.Terada, S.Nakamura, K.Shimizu
  • Journal Title: Proceedings of the 2011 International Conference on Bioscience, Biochemistry and Bioinformatics Pages: 342-347
  • Peer Reviewed
• [Journal Article] Protein-Protein Docking Using Multi-layered Spherical Basis Functions (2011)
  • Author(s): K.Sumikoshi
  • Journal Title: Proceedings of the 2011 International Conference on Bioscience, Biochemistry and Bioinformatics Pages: 342-347
  • Peer Reviewed
• [Journal Article] タンパク質の構造予測手法の開発 (2011)
  • Author(s): 清水謙多郎
  • Journal Title: 科学技術振興機構中国科学技術月報 Pages: 137-140
• [Journal Article] Prediction of carbohydrate-binding proteins from sequences using support vector machines. (2010)
  • Author(s): S.Someya, M.Kakuta, M.Morita, K.Sumikoshi, W.Cao, Z.Ge, O.Hirose, S.Nakamura, T.Terada, K.Shimizu
  • Journal Title: Advances in Bioinformatics Pages: 289301-289301
  • Peer Reviewed
• [Journal Article] Prediction of carbohydrate-binding proteins from sequences using support vector machines (2010)
  • Author(s): S.Someya
  • Journal Title: Advances in Bioinformatics Volume: 289301
  • Peer Reviewed
• [Journal Article] Molecular defect of isovaleryl-CoA dehydrogenase in the skunk mutant of silkworm, Bombyx mori. (2010)
  • Author(s): K.Urano
  • Journal Title: FEBS Journal Volume: 277 Pages: 4452-4463
  • Peer Reviewed
• [Journal Article] A self-organizing state space approach to infer time-varying causalities between regulatory proteins (2010)
  • Author(s): O.Hirose
  • Journal Title: Proceedings of International Conference on Information Technology in Bio- and Medcial Informatics, Lecture Notes in Computer Science Volume: 6266 Pages: 158-171
  • Peer Reviewed
• [Journal Article] Development of a retention time prediction method for HPLC and application to metabolome analysis (2010)
  • Author(s): T.Hagiwara
  • Journal Title: Bioinformation Volume: 5 Pages: 255-258
  • Peer Reviewed
• [Journal Article] Accurate prediction of native tertiary structure of protein using molecular dynamics simulation with the aid of the knowledge of secondary structures (2009)
  • Author(s): T.Furuta, K.Shimizu, T.Terada
  • Journal Title: Chemical Physics Letters 472 Pages: 134-139
  • Peer Reviewed
• [Journal Article] Comprehensive analysis of sequence-structure relationships in the loop regions of proteins (2009)
  • Author(s): S.Nakamura, K.Shimizu
  • Journal Title: GIW 2009 23 Pages: 106-116
  • Peer Reviewed
• [Journal Article] Computational Protocol for Screening GPI-anchored Proteins, Proceedings of the First International Conference on Bioinformatics and Computational Biology (BICoB) (2009)
  • Author(s): W.Cao, K.Sumikoshi, T.Terada, S.Nakamura, K.Kitamoto, K.Shimizu
  • Journal Title: Springer Lecture Notes in Bioinformatics Series 5462 Pages: 164-175
  • Peer Reviewed
• [Journal Article] Using a new GPI-anchored-protein identification system to mine the protein databases of Aspergillus fumigatus, Aspergillus nidulans, and Aspergillus oryzae (2009)
  • Author(s): W.Cao
  • Journal Title: J.Gen.Appl.Microbiol Volume: 55 Pages: 381-393
  • Peer Reviewed
• [Journal Article] A Generalized Conformational Energy Function of DNA Derived from Molecular Dynamics Simulations (2009)
  • Author(s): S.Yamasaki
  • Journal Title: Nucleic Acids Res Volume: 37
  • Peer Reviewed
• [Journal Article] Multicanonical ab inito QM/MM Molecular Dynamics Simulation of a Peptide in an Aqueous Environment (2009)
  • Author(s): R.Jono
  • Journal Title: J.Comput.Chem Volume: 31 Pages: 1168-1175
  • Peer Reviewed
• [Journal Article] Computational Protocol for Screening GPI-anchored Proteins (2009)
  • Author(s): W.Cao
  • Journal Title: Proceedings of the First International Conference on Bioinformatics and Computational Biology (BICoB), Springer Lecture Notes in Bioinformatics Series Volume: 5462 Pages: 164-175
  • Peer Reviewed
• [Journal Article] Anti-metatype peptides, a new molecular tool to monitor small ligands at high sensitivity and specificity (2009)
  • Author(s): J.Inaba
  • Journal Title: Analytical Biochemistry Volume: 388 Pages: 63-70
  • Peer Reviewed
• [Journal Article] Comprehensive analysis of sequence-structure relationships in the loop regions of proteins (2009)
  • Author(s): S.Nakamura
  • Journal Title: GIW 2009 Volume: 23 Pages: 106-116
  • Peer Reviewed
• [Journal Article] Ranking differentially expressed genes from Affymetrix gene expression data : methods with reproducibility, sensitivity, and specificity (2009)
  • Author(s): K.Kadota
  • Journal Title: Algorithms for Molecular Biology Volume: 4 Pages: 7-7
  • Peer Reviewed
• [Journal Article] Accurate prediction of native tertiary structure of protein using molecular dynamics simulation with the aid of the knowledge of secondary structures (2009)
  • Author(s): T.Furuta
  • Journal Title: Chemical Physics Letters Volume: 492 Pages: 134-139
  • Peer Reviewed
• [Journal Article] Accurate prediction of native tertiary structure of protein using molecular dynamics simulation with the aid of the knowledge of secondary structures (2009)
  • Author(s): Tadaomi Furuta, Kentaro Shimizu,Tohru Terada
  • Journal Title: Chemical Physics Letters 472 Pages: 134-139
  • Peer Reviewed
• [Journal Article] Prediction of protein-protein interaction sites using only sequence information and using both sequence and structural information (2008)
  • Author(s): M.Kakuta, S.Nakamura, K.Shimizu
  • Journal Title: IPSJ Transactions on Bioinformatics 49 Pages: 25-35
  • NAID: 110006684907
  • Peer Reviewed
• [Journal Article] Refinement of comparative models of protein structure by using multicanonical molecular dynamics simulations (2008)
  • Author(s): R.Ishitani, T.Terada, K.Shimizu
  • Journal Title: Molecular Simulation 34 Pages: 327-336
  • Peer Reviewed
• [Journal Article] Highly accurate method for ligand-binding site prediction in unbound state (apo) protein structures (2008)
  • Author(s): M.Morita, S.Nakamura, K.Shimizu
  • Journal Title: PROTEINS: Structure, Function, and Bioinformatics 73, 2 Pages: 468-479
  • Peer Reviewed
• [Journal Article] Refinement of comparative models of protein structure by using multicanonical molecular dynamics simulations (2008)
  • Author(s): Ryuuchiro Ishitani, Tohru Terada, Kehtaro Shimizu
  • Journal Title: Molecular Simulation 34 Pages: 327-336
  • Peer Reviewed
• [Journal Article] A compahson of generahzed Born methods in folding simulations (2008)
  • Author(s): Tohru Terada, Kentaro Shimizu
  • Journal Title: Chemical Physics Letters 460 Pages: 295-299
  • Peer Reviewed
• [Presentation] Finding genes related to the difference in drug-dose responses for multiple scle rosis disease by using a suneryised learnina annroach (2010)
  • Author(s): O.Hirose
  • Organizer: The 2010 Annual Conference of the Japanese Society for Bioinformatics (JSBi2010)
  • Place of Presentation: 福岡
  • Year and Date: 2010-12-14
• [Presentation] Carbohydrate-binding proteins : A sequence-based prediction model and the data base develonment (2010)
  • Author(s): W.Cao
  • Organizer: The 2010 Annual Conference of the Japanese Society for Bioinformatics (JSBi2010)
  • Place of Presentation: 福岡
  • Year and Date: 2010-12-13
• [Presentation] 絶対独立性好熱水素細菌Hydrogenobacter thermophilus TK-6のSerine hydroxyme thyltransferaseとアルドラーゼ活性 (2010)
  • Author(s): 千葉洋子
  • Organizer: 極限環境生物学会年会
  • Place of Presentation: 京都
  • Year and Date: 2010-11-16
• [Presentation] タンパク質-タンパク質ドッキングへの分子内フレキシビリティの導入 (2010)
  • Author(s): 角越和也
  • Organizer: 日本生物物理学会年会
  • Place of Presentation: 仙台
  • Year and Date: 2010-09-22
• [Presentation] タンパク質立体構造予測サーバおよびモデル構造の品質評価プラットフォームの開発 (2010)
  • Author(s): 中村周吾
  • Organizer: 日本生物物理学会年会
  • Place of Presentation: 仙台
  • Year and Date: 2010-09-22
• [Presentation] 二次構造情報を取り入れた分子動力学法によるタンパク質立体構造予測法の一般性の検証 (2010)
  • Author(s): 寺田透
  • Organizer: 日本生物物理学会年会
  • Place of Presentation: 仙台
  • Year and Date: 2010-09-21
• [Presentation] 糖鎖結合タンパク質の予測手法の開発 (2010)
  • Author(s): 葛臻翼
  • Organizer: 日本生物物理学会年会
  • Place of Presentation: 仙台
  • Year and Date: 2010-09-21
• [Presentation] Water interactions critically influence geometric and electronic structure of 2His-1 Carboxv Fe-redox centers : a auantum chemistry study (2010)
  • Author(s): W.Dawson
  • Organizer: 日本生物物理学会年会
  • Place of Presentation: 仙台
  • Year and Date: 2010-09-20
• [Presentation] Z-DNAを用いた核酸用力場の評価 (2010)
  • Author(s): 吉野惇志
  • Organizer: 日本生物物理学会年会
  • Place of Presentation: 仙台
  • Year and Date: 2010-09-20
• [Presentation] Carbohydrate-binding proteins : A sequence-based prediction model and the database development (2010)
  • Author(s): W.Cao, S.Someya, M.Kakuta, K.Sumikoshi, S.Nakamura, T.Terada, K. K. K.Shimizu
  • Organizer: The 2010 Annual Conference of the Japanese Society for Bioinformatics (JSBi2010)
  • Place of Presentation: 九州大学(福岡)
• [Presentation] タンパク質-タンパク質ドッキングへの分子内フレキシビリティの導入 (2010)
  • Author(s): 角越和也,中村周吾,清水謙多郎
  • Organizer: 日本生物物理学会第48回年会
  • Place of Presentation: 東北大学(宮城)
• [Presentation] 二次構造情報を取り入れた分子動力学法によるタンパク質立体構造予測法の一般性の検証 (2010)
  • Author(s): 寺田透,西村麻彦,清水謙多郎
  • Organizer: 日本生物物理学会第48回年会
  • Place of Presentation: 東北大学(宮城)
• [Presentation] The role of H-doping in the electronic structure, spin localization and electron transfer of iron-sulfur [2Fe-2S] proteins (2009)
  • Author(s): W.Dawson
  • Organizer: 日本生物物理学会第47回年会
  • Place of Presentation: 徳島
  • Year and Date: 2009-10-31
• [Presentation] バイオロジカルユニットを考慮したリガンド結合タンパク質データベースの構築 (2009)
  • Author(s): 池澤弘貴,森田瑞樹,清水謙多郎
  • Organizer: 日本生物物理学会第47回年会
  • Place of Presentation: 徳島文理大学(徳島)
• [Presentation] all-βタンパク質の二次構造拘束付きマルチカノニカル分子動力学シミュレーション (2009)
  • Author(s): 西村麻彦,寺田透,清水謙多郎
  • Organizer: 日本生物物理学会第47回年会
  • Place of Presentation: 徳島文理大学(徳島)
• [Presentation] An approach to protein-protein docking (2009)
  • Author(s): K.Sumikoshi
  • Organizer: International Symposium on Multi-scale Dynamics of Protein Complex Formation and Function
  • Place of Presentation: 東京
• [Presentation] 複数のサポートベクタマシンの組み合わせによるタンパク質局所構造予測法の開発 (2009)
  • Author(s): 中村周吾
  • Organizer: 日本生物物理学会第47回年会
  • Place of Presentation: 徳島
• [Presentation] アミノ酸側鎖のペプチド立体構造に及ぼす影響 (2009)
  • Author(s): 城野亮太
  • Organizer: 日本生物物理学会第47回年会
  • Place of Presentation: 徳島
• [Presentation] バイオロジカルユニットを考慮したリガンド結合タンパク質データベースの構築 (2009)
  • Author(s): 池澤弘貴
  • Organizer: 日本生物物理学会第47回年会
  • Place of Presentation: 徳島
• [Presentation] 計算的手法を用いた酵素設計:部位特異的変異によるパラ水酸化安息香酸水酸化酵素の基質特異性の改変 (2009)
  • Author(s): 飛田晃介
  • Organizer: 日本生物物理学会第47回年会
  • Place of Presentation: 徳島
• [Presentation] ベイズ統計学的解釈によるタンパク質-DNA認識におけるindirect readoutの評価 (2009)
  • Author(s): 山崎智
  • Organizer: 日本生物物理学会第47回年会
  • Place of Presentation: 徳島
• [Presentation] 分子動力学シミュレーションによるstaphylococcal protein AのB domainのフォールディング機構の研究 (2009)
  • Author(s): 西謙一郎
  • Organizer: 日本生物物理学会第47回年会
  • Place of Presentation: 徳島
• [Presentation] all-βタンパク質の二次構造拘束付きマルチカノニカル分子動力学シミュレーション (2009)
  • Author(s): 西村麻彦
  • Organizer: 日本生物物理学会第47回年会
  • Place of Presentation: 徳島
• [Presentation] A self-organizing state space approach to infer time-varying causalities between regulatory proteins (2009)
  • Author(s): 広瀬修
  • Organizer: 第12回情報論的学習理論ワークショップ
  • Place of Presentation: 福岡
• [Presentation] 生体分子の溶媒効果:マルチカノニカルQM/MM-MDによる研究 (2008)
  • Author(s): 城野亮太,渡邊佑輔,清水謙多郎,寺田透
  • Organizer: 日本生物物理学会第46回年会
  • Place of Presentation: 福岡
  • Year and Date: 2008-12-05
• [Presentation] ドメイン配列を用いたタンパク質間相互作用予測 (2008)
  • Author(s): 角田将典,角越和也,中村周吾,清水謙多郎
  • Organizer: 日本生物物理学会第46回年会
  • Place of Presentation: 福岡国際会議場(福岡)
• [Presentation] 生体分子の溶媒効果:マルチカノニカルQM/MM-MDによる研究 (2008)
  • Author(s): 城野亮太,渡邊佑輔,清水謙多郎,寺田透
  • Organizer: 日本生物物理学会第46回年会
  • Place of Presentation: 福岡国際会議場(福岡)
• [Presentation] 精密化プロセスを含めたタンパク質-タンパク質ドッキング手法の開発 (2008)
  • Author(s): 角越和也,寺田透,中村周吾,清水謙多郎
  • Organizer: 日本生物物理学会第46回年会
  • Place of Presentation: 福岡国際会議場(福岡)
• [Presentation] タンパク質構造予測 (2008)
  • Author(s): 清水謙多郎
  • Organizer: JSTゲノムリテラシー講座
  • Place of Presentation: JSTサイエンスプラザ(東京)
• [Presentation] タンパク質のオーダー・ディスオーダーループの配列構造相関の解析 (2008)
  • Author(s): 中村周吾,清水謙多郎
  • Organizer: 第8回日本蛋白質科学会年会
  • Place of Presentation: タワーホール船堀(東京)
• [Presentation] タンパク質ペアに対するカーネル関数を用いたタンパク質間相互作用予測 (2008)
  • Author(s): 角田将典,角越和也,中村周吾,清水謙多郎
  • Organizer: 第8回日本蛋白質科学会年会
  • Place of Presentation: タワーホール船堀(東京)
• [Presentation] 分子動力学シミュレーションによるWWドメインのフォールディング機構の解析 (2008)
  • Author(s): 西村麻彦,西謙一郎,寺田透,清水謙多郎
  • Organizer: 第8回日本蛋白質科学会年会
  • Place of Presentation: タワーホール船堀(東京)
• [Book] 中国科学技術月報第44号中国・日本科学最前線-研究の現場から-2011年版(タンパク質の構造予測手法の開発) (2011)
  • Author(s): 清水謙多郎
  • Publisher: 科学技術振興機構中国総合研究センター
• [Book] 遺伝子医学MOOK14次世代創薬テクノロジー実践:インシリコ創薬の最前線(タンパク質のabinitio構造予測) (2009)
  • Author(s): 中村周吾,清水謙多郎
  • Publisher: メディカルドゥ
• [Book] タンパク質のab initio構造予測 (2009)
  • Author(s): 中村周吾
  • Total Pages: 6
  • Publisher: メディカルドゥ
• [Remarks] ホームページ等
  • URL: http://www.bi.a.u-tokyo.ac.jp/~shimizu/
• [Remarks]
  • URL: http://www.bi.a.u-tokyo.ac.jp/