Research Topics
Genomes and GenesSpecies | Kengo KinoshitaSummaryAffiliation: Yokohama City University Country: Japan Publications
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Detail Information
Publications
Protein informatics towards function identificationKengo 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...- [Insight into the relation between protein structure and function]Kengo Kinoshita
Tanpakushitsu Kakusan Koso 47:1064-70. 2002 
Identification of protein biochemical functions by similarity search using the molecular surface database eF-siteKengo 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...- eF-site and PDBjViewer: database and viewer for protein functional sitesKengo 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..AVAILABILITY: The eF-site database and PDBjViewer are freely available from http://www.pdbj.org/eF-site/.. - Ring and zipper formation is the key to understanding the structural variety in all-beta proteinsRyotaro 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... - Crystal structure of the conserved protein TT1542 from Thermus thermophilus HB8Noriko 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... - Solution structure of the RWD domain of the mouse GCN2 proteinNobukazu 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... - PrDOS: prediction of disordered protein regions from amino acid sequenceTakashi 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... - PreBI: prediction of biological interfaces of proteins in crystalsYuko 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/... - eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shapeKengo 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)... - Docking of protein molecular surfaces with evolutionary trace analysisEiji 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)... - Intramolecular interaction of SUR2 subtypes for intracellular ADP-Induced differential control of K(ATP) channelsKenji 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... - Identification of transient hub proteins and the possible structural basis for their multiple interactionsMiho 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... 
Prediction of disordered regions in proteins based on the meta approachTakashi 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...- Protein structure databases with new web services for structural biology and biomedical researchDaron M Standley
Institute for Protein Research, Osaka University, Suita, Osaka 565 0871, Japan
Brief Bioinform 9:276-85. 2008.... - P-cats: prediction of catalytic residues in proteins from their tertiary structuresKengo Kinoshita
Institute of Medical Science, University of Tokyo, Shirokanedai, Minato ku, Tokyo 108 8639, Japan
Bioinformatics 21:3570-1. 2005..AVAILABILITY: P-cats is freely available at http://p-cats.hgc.jp/p-cats CONTACT: kino@ims.u-tokyo.ac.jp.. - Identification of the ligand binding sites on the molecular surface of proteinsKengo 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... - Identification of protein functions from a molecular surface database, eF-siteKengo 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... - Finding evolutionary relations beyond superfamilies: fold-based superfamiliesKeiko Matsuda
Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, 630-0101, Japan
Protein Sci 12:2239-51. 2003.... - Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfacesYuko Tsuchiya
Institute for Protein Research, Osaka University, Osaka, Japan
Proteins 55:885-94. 2004.... - Probabilistic description of protein alignments for sequences and structuresRyotaro 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... - ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in ArabidopsisTakeshi 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... - Key amino acid residues required for aryl migration catalysed by the cytochrome P450 2-hydroxyisoflavanone synthaseYuji 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... - Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservationMotonori 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... - Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairsHirokazu 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... - A cavity with an appropriate size is the basis of the PPIase activityTeikichi 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... - DBTGR: a database of tunicate promoters and their regulatory elementsNicolas 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... - 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 motifKengo 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... - Analyses of homo-oligomer interfaces of proteins from the complementarity of molecular surface, electrostatic potential and hydrophobicityYuko 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... - PreDs: a server for predicting dsDNA-binding site on protein molecular surfacesYuko Tsuchiya
Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
Bioinformatics 21:1721-3. 2005..Results of the prediction can be interactively checked with our original surface viewer. AVAILABILITY: PreDs is available free of charge from http://pre-s.protein.osaka-u.ac.jp/~preds/ CONTACT: ... - Probabilistic alignment detects remote homology in a pair of protein sequences without homologous sequence informationRyotaro 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... - Mutational analysis of block and facilitation of HERG current by a class III anti-arrhythmic agent, nifekalantYukio 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...