Functional annotation of innate immunity proteins

2011 Fiscal Year Final Research Report

• Project/Area Number: 21570169
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Biophysics
• Research Institution: Osaka University
• Principal Investigator: STANDLEY Daron 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)
• Project Period (FY): 2009 – 2011
• Keywords: Protein structure / protein function / threading / alignment

Research Abstract

A pipeline(SFAS) was constructed that predicts the location of functional domains based on several tools. Intrinsically disordered domains can be analyzed IDD Navigator. Structual domains can be analyzed using several novel methods have been developed by our group and integrated. In particular, sequence alignment(SEEKQUENCER, MAFFTash) and structure refinement(Spanner, OSCAR) show significant improvement over existing methods. The pipeline has been validated using large-scale benchmarks as well as case studies.

Research Products

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