Protein 3D structure Comparison
Protein 3D structure Prediction
Protein Sequence Analysis against complete genomes

Graduate School of Information Science, Room A501
Tel: +81-743-72-5396 / Fax : +81-743-72-5391

• Uehara K, Kawabata T, Go N. "Filtering remote homologues using predicted structural information". Protein Eng Des Sel., 17, 565-570,(2004). [MEDLINE]
• Kawabata,T. (2003) "MATRAS: A Program for Protein 3D Structure Comparison", Nucleic Acids Research, Vol. 31, pp. 3367-3369 [MEDLINE].
• Kawabata,T. and Nishikawa,K. (2000) "Protein structure comparison using the Markov transition model of evolution," Proteins, Vol 41, pp. 108-122. [MEDLINE]
• Kawabata,T., Fukuchi,S., Homma, K., Ota,M., Araki,J., Ito,T., Ichiyoshi, N. and Nishikawa, K.(2002) " GTOP:a database of protein structures predicted from genome sequences" Nucl. Acids Res., Vol.30, pp.294-298. [MEDLINE]
• Kawabata, T., Arisaka, F., and Nishikawa, K.(2000) "Structural/functional assignment of unknown bacteriophage T4 proteins by iterative database searches," Genes, Vol.259, pp. 223-233. [MEDLINE]
• Kawabata, T. and Doi, J.(1997) "Improvement of Protein Secondary Structure Prediction Using Binary W ord Encoding," Proteins, Vol 27, pp. 36-46. [MEDLINE]
• Kawabata,T., Ota,M., and Nishikawa,K. (1999) "The Protein Mutant Database" Nucleic Acids Research, Vol 27, 355-357. [PubMed] [Go to PMD page]
• Ota M., Kawabata T., Kinjo,R.A., Nishikawa,K.(1999) "Cooperative Approach for the Protein Fold Recognition" Proteins Suppl.3:126-132 [PubMed]
• Sagara,J., Shimizu,S., Kawabata,T., Nakamura,S., Ikeguchi,M., Shimizu,K.(1998) "The use of sequence comparison to detect identities in tRNA genes" Nucleic Acids Research, Vol 26, 1974-1979