自然免疫蛋白質の機能アノテーション

2011 年度 研究成果報告書

• 研究課題/領域番号: 21570169
• 研究種目: 基盤研究(C)
• 配分区分: 補助金
• 応募区分: 一般
• 研究分野: 生物物理学
• 研究機関: 大阪大学
• 研究代表者: スタンドレー ダーロン 大阪大学, 免疫学フロンティア研究センター, 特任准教授 (00448028)
• 研究期間 (年度): 2009 – 2011
• キーワード: Protein structure / protein function / threading / alignment

研究概要

抄録なし

研究成果

• [雑誌論文] Modeling the alternative oxidase from the human pathogen Blastocystis using automated hybrid structural template assembly (2012)
  • 著者名/発表者名: Standley DM, van der Giezen M
  • 雑誌名: Research and Reports in Biochemistry 巻: 2 ページ: 1-8
• [雑誌論文] Protein loop modeling with optimized backbone potential functions (2012)
  • 著者名/発表者名: Liang S, Zhang C, Sarmiento J, Standley DM
  • 雑誌名: J Chem Theory Comput 巻: (in press)
• [雑誌論文] Functional Annotation of Intrinsically Disordered Domains by Their Amino Acid Content Using Idd Navigator (2011)
  • 著者名/発表者名: Patil A, Teraguchi S, Dinh H, Nakai K, Standley DM
  • 雑誌名: Pac Symp Biocomput 巻: 17 ページ: 164-175
• [雑誌論文] Bridging the gap between single-template and fragment based protein structure modeling using Spanner (2011)
  • 著者名/発表者名: Lis M, Kim T, Sarmiento J, Kuroda D, Dinh H, Kinjo AR, Devadas S, Nakamura H, Standley DM
  • 雑誌名: Immunome Research 巻: 7
• [雑誌論文] Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions (2011)
  • 著者名/発表者名: Liang S, Zhou Y, Grishin N, Standley DM
  • 雑誌名: J COMPUT CHEM 巻: 32 ページ: 1680-1686
• [雑誌論文] Fast and accurate prediction of protein side-chain conformations (2011)
  • 著者名/発表者名: Liang S, Zheng D, Zhang C, Standley DM
  • 雑誌名: Bioinformatics 巻: 27 ページ: 2913-2914
• [雑誌論文] Protein loop selection using orientation-dependent force fields derived by parameter optimization (2011)
  • 著者名/発表者名: Liang S, Zhang C, Standley DM
  • 雑誌名: Proteins 巻: 79 ページ: 2260-2267
• [雑誌論文] Binding Energetics of Ferredoxin-NADP(+) Reductase with Ferredoxin and Its Relation to Function (2011)
  • 著者名/発表者名: Lee YH, Ikegami T, Standley DM, Sakurai K, Hase T, Goto Y
  • 雑誌名: ChemBioChem
• [雑誌論文] A mutation in the immunoproteasome subunit PSMB8 causes autoinflammation and lipodystrophy in humans (2011)
  • 著者名/発表者名: Kitamura A, Maekawa Y, Uehara H, Izumi K, Kawachi I, Nishizawa M, Toyoshima Y, Takahashi H, Standley DM, Tanaka K, et al
  • 雑誌名: J Clin Invest 巻: 121 ページ: 4150-4160
• [雑誌論文] Protein Data Bank Japan(PDBj): maintaining a structural data archive and resource description framework format (2011)
  • 著者名/発表者名: Kinjo AR, Suzuki H, Yamashita R, Ikegawa Y, Kudou T, Igarashi R, Kengaku Y, Cho H, Standley DM, Nakagawa A, Nakamura H
  • 雑誌名: Nucleic Acids Res 巻: 40 ページ: 453-460
• [雑誌論文] Intrinsically disordered domains deviate significantly from random sequences in mammalian proteins (2010)
  • 著者名/発表者名: Teraguchi S, Patil A, Standley DM
  • 雑誌名: BMC Bioinformatics 巻: S7 ページ: 11
• [雑誌論文] SeSAW balancing sequence and structural information in protein functional mapping (2010)
  • 著者名/発表者名: Standley DM, Yamashita R, Kinjo AR, Toh H, Nakamura H
  • 雑誌名: Bioinformatics 巻: 26 ページ: 1258-1259
• [雑誌論文] The DBCLS BioHackathon : standardization and interoperability for bioinformatics web services and workflows (2010)
  • 著者名/発表者名: Katayama T, Arakawa K, Nakao M, Ono K, K. F A-K, Yamamoto Y, Aerts J, Aranda B, Barboza LH, Bonnal R, (+ 36 authors), Standley DM, (+ 10 authors)
  • 雑誌名: Journal of Biomedical Semantics 巻: 1
• [雑誌論文] Ab initio simulation of a 57-residue protein in explicit solvent reproduces the native conformation in the lowest free-energy cluster (2010)
  • 著者名/発表者名: Ikebe J, Standley DM, Nakamura H, Higo J
  • 雑誌名: Protein Science 巻: 20 ページ: 187-196
• [雑誌論文] A single polymorphic amino acid on Toxoplasma gondii kinase ROP16 determines the direct and strain-specific activation of Stat3 (2009)
  • 著者名/発表者名: Yamamoto M, Standley DM, Takashima S, Saiga H, Okuyama M, Kayama H, Kubo E, Ito H, Takaura M, Matsuda T, et al
  • 雑誌名: J Exp Med 巻: 206 ページ: 2747-2760
• [雑誌論文] Outcome of a workshop on applications of protein models in biomedical research (2009)
  • 著者名/発表者名: Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV(+ 16 authors), Standley DM, (+ 5 authors)
  • 雑誌名: Structure 巻: 17 ページ: 151-159
• [雑誌論文] Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay (2009)
  • 著者名/発表者名: Matsushita K, Takeuchi O, Standley DM, Kumagai Y, Kawagoe T, Miyake T, Satoh T, Kato H, Tsujimura T, Nakamura H, Akira S
  • 雑誌名: Nature 巻: 458 ページ: 1185-1190
• [雑誌論文] Membrane attachment facilitates ligand access to the active site in monoamine oxidase A (2009)
  • 著者名/発表者名: Apostolov R, Yonezawa Y, Standley DM, Kikugawa G, Takano Y, Nakamura H
  • 雑誌名: Biochemistry 巻: 48 ページ: 5864-5873
• [学会発表] Functional Annotation of Intrinsically Disordered Domains by Their Amino Acid Content Using IDD Navigator (2012)
  • 著者名/発表者名: Standley DM
  • 学会等名: Pacific Symposium on Biocomputing
  • 発表場所: Hawaii, USA
  • 年月日: 2012-01-06
• [学会発表] A structural view of Innate immunity (2011)
  • 著者名/発表者名: Standley DM
  • 学会等名: Dana-Farber Cancer Institute
  • 発表場所: Cancer Vaccine Center, USA
  • 年月日: 20110300
• [学会発表] Prediction of dinucleotide-specific RNA-binding sites in proteins (2011)
  • 著者名/発表者名: Standley DM
  • 学会等名: Malaysia
  • 発表場所: Kuala Lumpur
  • 年月日: 2011-11-14
• [学会発表] Function prediction of structured and unstructured proteins (2011)
  • 著者名/発表者名: Standley DM
  • 学会等名: China 5th China Medical Biotech Forum(CMBF-2011)
  • 発表場所: Beiing
  • 年月日: 2011-11-08
• [学会発表] Restrained docking of protein molecular surfaces (2010)
  • 著者名/発表者名: Standley DM
  • 学会等名: Department of Chemistry
  • 発表場所: New York, USA : Columbia Univ
  • 年月日: 20101100
• [学会発表] An introduction to protein-protein docking II (2009)
  • 著者名/発表者名: Standley DM
  • 学会等名: Predictive Biology lecture series
  • 発表場所: Tokyo, Japan : Ochanomizu Univ
  • 年月日: 20091100
• [学会発表] Functional Annotation using SeSAW (2009)
  • 著者名/発表者名: Standley DM
  • 学会等名: MEI Center lecture series
  • 発表場所: Osaka, Japan
  • 年月日: 20091100
• [備考]
  • URL: http://sysimm.ifrec.osaka-u.ac.jp/