Master Thesis

• 2002
  • Katsunori Uehara Development of a method for Protein Remote Homologue Detection Using Secondary Structure Prediction and Solvent Accessibility Prediction.

Latest Publications

• 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]

References

• 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�h 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. �gConformational 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]