Kengo Kinoshita

Summary

Affiliation: Yokohama City University
Country: Japan

Publications

  1. ncbi request reprint Protein informatics towards function identification
    Kengo Kinoshita
    Graduate School of Integrated Science, Yokohama City University, 1 7 29 Suehiro cho, Turumi ku, 230 0045, Yokohama, Japan
    Curr Opin Struct Biol 13:396-400. 2003
  2. ncbi request reprint [Insight into the relation between protein structure and function]
    Kengo Kinoshita
    Tanpakushitsu Kakusan Koso 47:1064-70. 2002
  3. pmc Identification of protein biochemical functions by similarity search using the molecular surface database eF-site
    Kengo Kinoshita
    Graduate School of Integrated Science, Yokohama City University, Yokohama 230 0045, Japan
    Protein Sci 12:1589-95. 2003
  4. ncbi request reprint eF-site and PDBjViewer: database and viewer for protein functional sites
    Kengo Kinoshita
    Graduate School of Integrated Science, Yokohama City University, 1 7 29 Suehiro cho, Tsurumi ku, Yokohama, 230 0045, Japan
    Bioinformatics 20:1329-30. 2004
  5. ncbi request reprint Ring and zipper formation is the key to understanding the structural variety in all-beta proteins
    Ryotaro Koike
    Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake cho, Sakyo ku, Kyoto, 606 8502, Japan
    FEBS Lett 533:9-13. 2003
  6. pmc Crystal structure of the conserved protein TT1542 from Thermus thermophilus HB8
    Noriko Handa
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Protein Sci 12:1621-32. 2003
  7. pmc Solution structure of the RWD domain of the mouse GCN2 protein
    Nobukazu Nameki
    RIKEN Genomic Sciences Center, Tsurumi, Yokohama, Japan
    Protein Sci 13:2089-100. 2004
  8. pmc PrDOS: prediction of disordered protein regions from amino acid sequence
    Takashi Ishida
    Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo, 108 8639, Japan
    Nucleic Acids Res 35:W460-4. 2007
  9. pmc PreBI: prediction of biological interfaces of proteins in crystals
    Yuko Tsuchiya
    Institute for Protein Research, Osaka University, 3 2 Yamadaoka, Suita, Osaka, 565 0871, Japan
    Nucleic Acids Res 34:W320-4. 2006
  10. pmc eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape
    Kengo Kinoshita
    Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minatoku, Tokyo, 108 8639, Japan
    Nucleic Acids Res 35:W398-402. 2007

Collaborators

Detail Information

Publications32

  1. ncbi request reprint Protein informatics towards function identification
    Kengo Kinoshita
    Graduate School of Integrated Science, Yokohama City University, 1 7 29 Suehiro cho, Turumi ku, 230 0045, Yokohama, Japan
    Curr Opin Struct Biol 13:396-400. 2003
    ..The importance of heterogeneous databases and various descriptors of amino acid sequences, tertiary structures and pathways on the proteome scale has been emphasised...
  2. ncbi request reprint [Insight into the relation between protein structure and function]
    Kengo Kinoshita
    Tanpakushitsu Kakusan Koso 47:1064-70. 2002
  3. pmc Identification of protein biochemical functions by similarity search using the molecular surface database eF-site
    Kengo Kinoshita
    Graduate School of Integrated Science, Yokohama City University, Yokohama 230 0045, Japan
    Protein Sci 12:1589-95. 2003
    ..We also applied our method to a hypothetical protein, MJ0226 from Methanococcus jannaschii, and detected the mononucleotide binding site from the similarity to other proteins having different folds...
  4. ncbi request reprint eF-site and PDBjViewer: database and viewer for protein functional sites
    Kengo Kinoshita
    Graduate School of Integrated Science, Yokohama City University, 1 7 29 Suehiro cho, Tsurumi ku, Yokohama, 230 0045, Japan
    Bioinformatics 20:1329-30. 2004
    ..To enable browsing of each molecular surface along with the atomic model, we have developed a new three-dimensional interactive viewer, PDBjViewer, that can be used both as an applet and as a stand-alone program...
  5. ncbi request reprint Ring and zipper formation is the key to understanding the structural variety in all-beta proteins
    Ryotaro Koike
    Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake cho, Sakyo ku, Kyoto, 606 8502, Japan
    FEBS Lett 533:9-13. 2003
    ..We discuss the implication of the unexpectedly high preference for the ring and zippered structures in connection with the folding process of beta proteins...
  6. pmc Crystal structure of the conserved protein TT1542 from Thermus thermophilus HB8
    Noriko Handa
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Protein Sci 12:1621-32. 2003
    ..TT1542 is a homohexamer in the crystal and in solution, the six monomers forming a cylindrical structure. Putative active sites are suggested by the structure and conserved amino acid residues...
  7. pmc Solution structure of the RWD domain of the mouse GCN2 protein
    Nobukazu Nameki
    RIKEN Genomic Sciences Center, Tsurumi, Yokohama, Japan
    Protein Sci 13:2089-100. 2004
    ..Thus, it appears that the RWD domain is a novel structural domain for protein-binding that plays specific roles in individual RWD-containing proteins...
  8. pmc PrDOS: prediction of disordered protein regions from amino acid sequence
    Takashi Ishida
    Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo, 108 8639, Japan
    Nucleic Acids Res 35:W460-4. 2007
    ..The prediction results are sent by e-mail, and the server also provides a web-interface to check the results...
  9. pmc PreBI: prediction of biological interfaces of proteins in crystals
    Yuko Tsuchiya
    Institute for Protein Research, Osaka University, 3 2 Yamadaoka, Suita, Osaka, 565 0871, Japan
    Nucleic Acids Res 34:W320-4. 2006
    ..The results can be checked through an interactive viewer, and the most probable complex can be downloaded as atomic coordinates in the PDB format. PreBI is available at http://pre-s.protein.osaka-u.ac.jp/~prebi/...
  10. pmc eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape
    Kengo Kinoshita
    Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minatoku, Tokyo, 108 8639, Japan
    Nucleic Acids Res 35:W398-402. 2007
    ..In addition, the predicted interacting interface is displayed to facilitate the examination of the virtual complex structure on our own applet viewer with the web browser (URL: http://eF-site.hgc.jp/eF-seek)...
  11. ncbi request reprint Docking of protein molecular surfaces with evolutionary trace analysis
    Eiji Kanamori
    Japan Biological Information Research Center, Japan Biological Informatics Consortium, 2 41 6 Aomi, Koto ku, Tokyo 135 0064, Japan
    Proteins 69:832-8. 2007
    ..In addition, we have analyzed the feasibility of the ET method for docking simulations, and found that the conservation information was useful only in a limited category of proteins (signal related proteins and enzymes)...
  12. ncbi request reprint Intramolecular interaction of SUR2 subtypes for intracellular ADP-Induced differential control of K(ATP) channels
    Kenji Matsushita
    Department of Pharmacology II, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
    Circ Res 90:554-61. 2002
    ..Therefore, the interaction might be involved in the control of ADP-induced differential activation of SUR2-subtype K(ATP) channels...
  13. pmc Identification of transient hub proteins and the possible structural basis for their multiple interactions
    Miho Higurashi
    Institute of Medical Science, The University of Tokyo, Tokyo, Japan
    Protein Sci 17:72-8. 2008
    ..We also found greater predominance of charged and polar residues in sociable proteins than previously reported...
  14. doi request reprint Prediction of disordered regions in proteins based on the meta approach
    Takashi Ishida
    Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Bioinformatics 24:1344-8. 2008
    ..As a result, the meta approach achieved higher prediction accuracy than all methods participating in CASP7...
  15. doi request reprint Protein structure databases with new web services for structural biology and biomedical research
    Daron M Standley
    Institute for Protein Research, Osaka University, Suita, Osaka 565 0871, Japan
    Brief Bioinform 9:276-85. 2008
    ....
  16. ncbi request reprint P-cats: prediction of catalytic residues in proteins from their tertiary structures
    Kengo Kinoshita
    Institute of Medical Science, University of Tokyo, Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Bioinformatics 21:3570-1. 2005
    ..The reply contains a summary and two URLs to allow the user to examine the conserved residues: one for interactive images of the prediction results and the other for a graphical view of the multiple sequence alignment...
  17. pmc Identification of the ligand binding sites on the molecular surface of proteins
    Kengo Kinoshita
    The Institute of Medical Science, The University of Tokyo, 4 6 1, Shirokanedai, Minato ku, Tokyo, 108 8639, Japan
    Protein Sci 14:711-8. 2005
    ..Finally, we extensively applied our method to newly determined hypothetical proteins, including some without annotations, and evaluated the performance of our methods...
  18. ncbi request reprint Identification of protein functions from a molecular surface database, eF-site
    Kengo Kinoshita
    Institute for Protein Research, Osaka University, 3 2 Yamadaoka, Suita, Osaka 565 0871, Japan
    J Struct Funct Genomics 2:9-22. 2002
    ..The method identifies the active site having the similar function to those of the known proteins...
  19. pmc Finding evolutionary relations beyond superfamilies: fold-based superfamilies
    Keiko Matsuda
    Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, 630 0101, Japan
    Protein Sci 12:2239-51. 2003
    ....
  20. ncbi request reprint Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces
    Yuko Tsuchiya
    Institute for Protein Research, Osaka University, Osaka, Japan
    Proteins 55:885-94. 2004
    ....
  21. ncbi request reprint Probabilistic description of protein alignments for sequences and structures
    Ryotaro Koike
    Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake cho, Sakyo ku, Kyoto 606 8502, Japan
    Proteins 56:157-66. 2004
    ..It was shown that the sequence and structure alignments are consistent with each other and that the alignments with the highest probability represent circular permutation...
  22. pmc ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis
    Takeshi Obayashi
    Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 B 14 Nagatsuta cho, Midori ku, Yokohama 226 8501, Japan
    Nucleic Acids Res 35:D863-9. 2007
    ..ATTED-II can thus help researchers to clarify the function and regulation of particular genes and gene networks...
  23. ncbi request reprint Key amino acid residues required for aryl migration catalysed by the cytochrome P450 2-hydroxyisoflavanone synthase
    Yuji Sawada
    Department of Applied Biological Sciences, Nihon University, Fujisawa, Kanagawa 252 8510, Japan
    Plant J 31:555-64. 2002
    ..The roles of these amino acid residues in the catalysis and evolution of isoflavonoid biosynthesis are discussed...
  24. ncbi request reprint Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation
    Motonori Ota
    National Institute of Genetics, Yata, Mishima, 411 8540, Shizuoka, Japan
    J Mol Biol 327:1053-64. 2003
    ..We applied it to some so-called "hypothetical" proteins, with known structures but undefined functions. The relationships among the catalytic, conserved, and destabilizing residues in enzymatic proteins are discussed...
  25. pmc Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs
    Hirokazu Chiba
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    BMC Genomics 9:152. 2008
    ..A number of studies have compared protein sequences or promoter sequences between mammals, which provided many insights into genomics. However, the correlation between protein conservation and promoter conservation remains controversial...
  26. doi request reprint A cavity with an appropriate size is the basis of the PPIase activity
    Teikichi Ikura
    Laboratory of Structural Biology, School of Biomedical Science, Tokyo Medical and Dental University, 1 5 45 Yushima, Tokyo 113 8510, Japan
    Protein Eng Des Sel 21:83-9. 2008
    ..These results suggest that a cavity with an appropriate size is the basis of the PPIase activity...
  27. pmc DBTGR: a database of tunicate promoters and their regulatory elements
    Nicolas Sierro
    Human Genome Center, The Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 34:D552-5. 2006
    ..At the time of writing, information about 184 promoters, containing 73 identified binding sites and >2000 newly predicted binding sites is available. This database is accessible at http://dbtgr.hgc.jp...
  28. ncbi request reprint Analysis of the three dimensional structure of the CXGXC motif in the CMGCC and CAGYC regions of alpha-and beta-subunits of human chorionic gonadotropin: importance of glycine residue (G) in the motif
    Kengo Kinoshita
    Japan Science Corporation
    Endocr J 53:51-8. 2006
    ..The significance of similar motifs found in various human proteins other than glycoprotein hormones was suggested...
  29. ncbi request reprint Analyses of homo-oligomer interfaces of proteins from the complementarity of molecular surface, electrostatic potential and hydrophobicity
    Yuko Tsuchiya
    Institute for Protein Research, Osaka University, Suita, Osaka 565 0871, Japan
    Protein Eng Des Sel 19:421-9. 2006
    ..In addition, we also show that complementarity analyses can be used to discriminate the biological-interface from the crystallographic-interface in homo-oligomer proteins...
  30. ncbi request reprint PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces
    Yuko Tsuchiya
    Institute for Protein Research, Osaka University, 3 2 Yamadaoka, Suita, Osaka, 565 0871, Japan
    Bioinformatics 21:1721-3. 2005
    ..The prediction was done by evaluating the electrostatic potential, the local curvature and the global curvature on the surfaces. Results of the prediction can be interactively checked with our original surface viewer...
  31. ncbi request reprint Probabilistic alignment detects remote homology in a pair of protein sequences without homologous sequence information
    Ryotaro Koike
    Global Scientific Information and Computing Center, Tokyo Institute of Technology, Ookayama, Tokyo 152 8550, Japan
    Proteins 66:655-63. 2007
    ..PA successfully detected sequence homologues for the two proteins and confirmed that the observed structural similarities are the result of an evolutional relationship...
  32. ncbi request reprint Mutational analysis of block and facilitation of HERG current by a class III anti-arrhythmic agent, nifekalant
    Yukio Hosaka
    Department of Pharmacology, Graduate School of Medicine, Osaka University, Osaka, Japan
    Channels (Austin) 1:198-208. 2007
    ..Further mutations and flexible-docking simulations suggest that the size, but not the polarity, of the side chain at S649 is critical for drug induced facilitation...