修士論文

• 平成１６年度
  • 及川雅隆 Ramachandranプロットを用いた分子モデルの妥当性の評価 ー 評価に用いる領域の検討 ー

  • 山極裕道 酵素の触媒残基予測に向けたアミノ酸配列・立体構造に関する統計解析

• 平成１５年度
  • 石部大介 予測構造とモチーフ情報を利用したタンパク質配列間の弱い相同性の検出法の開発

  • 谷本心 Analysis of Transmembrane Helices in Proteins : The Difficult-to-predict Helices

  • 福原直志 表面アミノ酸分布を用いたタンパク質間相互作用サイトの予測法の開発

• 平成１４年度
  • 植原　克典 ２次構造予測等を利用したタンパク質間の弱いアミノ酸配列相同性を検出する手法の開発

研究業績

最近の発表論文

• Uehara K, Kawabata T, Go N. "Filtering remote homologues using predicted structural information". Protein Eng Des Sel., 17, 565-570,(2004). [MEDLINE]

• Basu G, Sivanesan D, Kawabata T, Go N. "Electrostatic Potential of Nucleotide-free Protein is Sufficient for Discrimination Between Adenine and Guanine-specific Binding Sites", J Mol Biol. 342,1053-1066 (2004). [MEDLINE]

• Kawabata,T. "MATRAS: A Program for Protein 3D Structure Comparison", Nucleic Acids Research, 31, 3367-3369, (2003). [MEDLINE].

• Matsuda,K., Nishioka,T., Kinoshita, K., Kawabata,T., Go,N. "Finding evolutionary relations beyond superfamilies: Fold-based Superfamilies". Protein Science, vol 12, 2239-2251, (2003). [MEDLINE]

• Nakamura,K., Kawabata,T., Yura,K., Go, N. "Novel types of two-domain multi-copper oxidases: Possible missing links in the evolution", FEBS Letters, vol 553, 2329-244, (2003) [MEDLINE]

• Pal,L., Chakrabarti,P., Basu,G. "Sequence and structure patterns in proteins from an analysis of the shortest helices: implications for helix nucleation", J Mol. Biol. Vol. 326, 273-91 (2003). [MEDLINE]

主な発表論文

• Kawabata,T. and Nishikawa,K. "Protein tertiary structure comparison using the Markov transition model of evolution," Proteins, Vol 41, pp. 108-122, 2000. [MEDLINE]
• Kawabata,T., Fukuchi,S., Homma, K., Ota,M., Araki,J., Ito,T., Ichiyoshi, N. and Nishikawa, K."GTOP:a database of protein structures predicted from genome sequences" Nucl. Acids Res., Vol.30, pp.294-298, 2002. [MEDLINE]
• Kawabata, T., Arisaka, F., and Nishikawa, K. "Structural/functional assignment of unknown bacteriophage T4 proteins by iterative database searches," Genes, Vol.259, pp. 223-233, 2000. [MEDLINE]
• Kawabata, T. and Doi, J. "Improvement of Protein Secondary Structure Prediction Using Binary Word Encoding," Proteins, Vol 27, pp. 36-46, 1997. [MEDLINE]
• Basu, G., Kitao, A., Kuki, A. and Go, N. "Protein Electron Transfer Reorganization Energy Spectrum from Normal Mode Analysis. I. Theory" J. Phys. Chem B, 102, 2076-2084 (1998).
• Basu, G., Kitao, A., Kuki, A., and Go, N. "Protein Electron Transfer Reorganization Energy Spectrum from Normal Mode Analysis. II. Application to Ru-modified Cytochrome c" J. Phys. Chem B , Vol. 102, pp 2085-2094, 1998.
• Pal, L. & Basu, G. "Novel protein structural motifs containing two-turn and longer 310-helices" Protein Eng. Vol. 12, pp 811-814 , 1999. [MEDLINE]
• Kettani, A., Basu, G., Gorin, A., Majumdar, A., Skripkin, E. and Patel, D. J. "A two-stranded template-based approach to G.(C-A) triad formation: designing novel structural elements into an existing DNA framework" J. Mol. Biol., Vol. 301, pp 129-146, 2000.
• Pal, L. and Basu, G. "Neural Network Prediction of 310-helices in proteins” Ind. J. Biochem. Biophys. 38, pp 107-114, 2001. [MEDLINE]
• Sengupta, J., Ray, P. K. and Basu, G. "Solution structure of an immunoactive peptide from Staphylococcal Protein A" J. Biomol. Struct. Dyn. 18, pp 773-81, 2001.
• Pal, D., Mahapatra, P., Manna, T., Chakrabarti, P., Bhattacharyya, B., Banerjee, A., Basu, G. and Roy, S. “Conformational properties of alpha-tubulin tail peptide: Implications for tail-body interaction" Biochemistry 40, pp 15512-15519, 2001.
• Ghose, M., Mandal, S., Roy, D., R. K. Mandal and Basu, G. "Dielectric Relaxation in a Single Tryptophan Protein" FEBS Lett. 509, pp 337-340, 2001.
• Kinoshita, K., Kidera, A., and Go,N. "Diversity of functions of proteins with internal symmetry in spatial arrangement of secondary structural elements". Protein Science Vol.8, No.6,pp 1210-1217, 1999. [MEDLINE]
• Kinoshita, K., Sadanami, K., Kidera, A. and Go,N. "Structural motif of phosphate-binding site common to various protein superfamilies : all-against-all structure comparison of protein-mononucleotide complexes" Protein Engineering, vol.12,No.1, pp.11-14, 1999. [MEDLINE]