Computational Biology Research Center[CBRC]

Gromiha, M. M., Ahmad, Shandar: "Role of Solvent Accessibility in Structure Based Drug Design", Current Computer Aided Drug Design, 1, pp.223-235 (2005).
Gromiha, M.M., Suwa, M.: "Structural analysis of residues involving cation-pi interactions in different folding types of membrane proteins", INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES, 35, pp.55-62 (2005).■PDF(152KB)
Gromiha, M. M.: "Distinct roles of conventional non-covalent and cation-pi interactions in protein stability", POLYMER, 46(3), pp.983-990 (2005).
Demura, M., Yoshida, T., Hirokawa, T., Kumaki, Y., Aizawa, T., Nitta, K., Bitter, I., T?th, K.: "Interaction of dopamine and acetylcholine with an amphiphilic resorcinarene receptor in organic solvent and in aqueous sodium dodecylsulfate micelle system: An NMR study", BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 15(5), pp.13 (2005). ■Abstract on ScienceDirect website
Saraboji K, Gromiha MM, Ponnuswamy MN.: "Relative importance of secondary structure and solvent accessibility to the stability of protein mutants. A case study with amino acid properties and energetics on T4 and human lysozymes", COMPUTERS & CHEMISTRY (Presently Computational Biology and Chemistry), 29(1), pp.25-35 (2005).■PDF(168KB)
Katada,S., Hirokawa T., Oka, Y., Makiko Suwa,2 and Kazushige Touhara: "Structural Basis for a Broad But Selective Ligand Spectrum of a Mouse Olfactory Receptor: Mapping the Odorant-Binding Site", JOURNAL OF NEUROSCIENCE, 25(7), pp.1806-1815 (2005).■PDF(739KB)
Machida, M., et al. (incl. Asai, K., Kumagai, T., Terai, G., Gotoh, O., Kin, T., Nagasaki, H., Okada, K. from CBRC): "Genome sequencing and analysis of Aspergillus oryzae", Nature, 438, pp.1157-1161 (2005). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Galagan, J.E., et al. (incl. Kumagai, T., Asai, K. from CBRC): "Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae", Nature, 438, pp.1105-1115 (2005). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Nierman, W., et al. (incl. Kumagai, T., Asai, K. from CBRC): "Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus", Nature, 438, pp.1151-1156 (2005). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Ono, Y., Fujibuchi, W., Suwa, M.: "Automatic gene collection system for genome-scale overview of G-protein coupled receptors in eukaryotes", Gene, 364, pp.63-73 (2005). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Gromiha, M.M., Siebers, J.G., Selvaraj, S., Kono, H., Sarai, A.: "Role of inter and intramolecular interactions in protein-DNA recognition", Gene, 364, pp.108-113 (2005). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Nagasaki, H., Arita, M., Nishizawa, T., Suwa, M., Gotoh, O.: "Species-specific variation of alternative splicing and transcriptional initiation in six eukaryotes", Gene, 364, pp.53-62 (2005). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
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Park, KJ., Gromiha, M.M., Horton, P., Suwa, M.: "Discrimination of outer membrane proteins using support vector machines", Bioinformatics, 21(23), pp.4223-4229 (2005). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Nakashima-Kamimura, N., et al. (incl. Mukai, Y. from CBRC): "MIDAS/GPP34, a nuclear gene product, regulates total mitochondrial mass in response to mitochondrial dysfunction", Journal of Cell Science, 118(Pt 22), pp.5357-5367 (2005). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Tsukamoto, K., Watanabe, T., Nagashimab, U., Akiyama, Y.: "Hartree-Fock and density functional theory calculations for the reaction mechanism of nitric oxide reductase cytochrome P450nor from Fusarium oxysporum", Journal of Molecular Structure: THEOCHEM, 732(1-3), pp.87-98 (2005). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal.
Fujibuchi, W., Kiseleva, L., Taniguchi, T., Horton, P.: "Development of Cell Knowledge Base and Prediction of Cell Types and Characteristics by Gene Expression Profiles", IPS: SIG Technical Reports, 99, pp.33-37 (2005). (In Japanese)
Tsuda, K., Shin, H., Scholkopf, B.: "Fast protein classification with multiple networks", Bioinformatics, 21(Suppl 2), pp.ii59-ii65 (2005). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Tomii, K., Hirokawa, T., Motono, C.: "Protein structure prediction using a variety of profile libraries and 3D verification", Proteins, 61(Supple 7), pp.114-121 (2005). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
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Gromiha, M.M.: "Motifs in outer membrane protein sequences: applications for discrimination", Biophysical Chemistry, 117(1), pp.65-71 (2005). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Terashima, Y., Onai, N., Murai, M., Enomoto, M., Poonpiriya, V., Hamada, T., Motomura, K., Suwa, M., Ezaki, T., Haga, T., Kanegasaki, S., Matsushima, K.: "Pivotal function for cytoplasmic protein FROUNT in CCR2-mediated monocyte chemotaxis", Nature Immunology, 6(8), pp.827-835 (2005). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Tsuda, K.: "Propagating Distributions on a Hypergraph by Dual Information Regularization", Conceptual Modeling -- ER 2003 22nd International Conference on Conceptual Modeling, Chicago, IL, USA, October 13-16, 2003, Proceedings, pp.921-928 (2005).
Yabuki, Y., Muramatsu, T., Hirokawa, T., Mukai, H., Suwa, M.: "GRIFFIN: a system for predicting GPCR-G-protein coupling selectivity using a support vector machine and a hidden Markov model", Nucleic Acids Research, 33(Web Server issue), pp.W148-W153 (2005). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Jeong, M.J., Lee, J.S.: "Shape Design of Passages of Turbin Blade Using Design Opimization System", Transactions of the KSME, Part A, 29(7), pp.1013-1021 (2005).
Magyar, C., Gromiha, M.M., Pujadas, G., Tusnady, G.E., Simon, I.: "SRide: a server for identifying stabilizing residues in proteins", Nucleic Acods Research, 33(Web Server issue), pp.W303-W305 (2005). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
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Gromiha, M.M., Ahmad, S., Suwa, M.: "TMBETA-NET: discrimination and prediction of membrane spanning beta-strands in outer membrane proteins", Nucleic Acods Research, 33(Web Server issue), pp.W164-W167 (2005). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Gotoh, O., Nagasaki, H.: "(In Japanese)", Doubutsu Iden Ikusyu Kenkyu, 32(2), pp.39-46 (2005). (In Japanese)
Tsuda, K., Ratsch, G.: "Image reconstruction by linear programming", Image Processing, IEEE Transactions on, 14(6), pp.737-744 (2005). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal.
Tsuda, K., Ratsch, G., Warmuth, M.K.: "Matrix Exponentiated Gradient Updates for On-line Learning and Bregman Projection", Journal of Machine Learning Research, 6(Jun), pp.995-1018 (2005). ■Free Full Text Paper(PDF) on the Journal Website.
Fukuda, K.: "(In Japanese)", Jikken Igaku Zoukango, 23(11), pp.171-177 (2005). (In Japanese)
Horton, P., Fujibuchi, W.: "An Upper Bound on the Hardness of Exact Matrix Based Motif Discovery", Lecture Notes in Computer Science, 3537, pp.219-228 (2005). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal.
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Fukuda, K.: "Higher Order Knowledge Proceeding:Pathway Database and Ontologies", Genomics & Informatics, 3(2), pp.47-51 (2005).
Ikeda, K., Tomii, K., Yokomizo, T., Mitomo, D., Maruyama, K., Suzuki, S., Higo, J.: "Visualization of conformational distribution of short to medium size segments in globular proteins and identification of local structural motifs", Protein Science, 14(5), pp.1253-1265(2005). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Aita, T., Morinaga, S., Husimi, Y.: "Thermodynamical interpretation of evolutionary dynamics on a fitness landscape in an evolution reactor, II", Bulletin of Mathematical Biology, 67(3), pp.613-635 (2005). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Gromiha, M.M.: "Influence of DNA stiffness in protein-DNA recognition", Journal of Biotechnology, 117(2), pp.137-145 (2005). ■Full Text Paper(PDF) on the Journal Website. You need the license for the electrical journal. ■PubMed
Okada, K., Kanaya, S., Asai, K.: "Accurate extraction of functional associations between proteins based on common interaction partners and common domains", Bioinformatics, 21(9), pp.2043-2048 (2005). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Nakao, M., Barrero, R.A., Mukai, Y., Motono, C., Suwa, M., Nakai, K.: "Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals", Nucleic Acids Research, 33(8), pp.2355-2363 (2005). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
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Gromiha, M.M., Suwa, M.: "A simple statistical method for discriminating outer membrane proteins with better accuracy", Bioinformatics, 21(7), pp.961-968 (2005). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Kiryu, H., Oshima, T., Asai, K.: "Extracting relations between promoter sequences and their strengths from microarray data", Bioinformatics, 21(7), pp.1062-1068 (2005). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed
Nagano, N.: "EzCatDB: the Enzyme Catalytic-mechanism Database", Nucleic Acids Research, 33(Database issue), pp.D407-412 (2005). ■Free Full Text Paper(PDF) on the Journal Website. ■PubMed

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