Genomes and Genes
Affiliation: Yokohama City University
- 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: email@example.com..
- 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...