Associate Professor
	Takeshi Kawabata

Last Modified : Mar 31, 2011

• Research

  Structural Bioinformatics
  Detection of binding pocket on protein surface
  Modeling of protein complexes guided by low-resolution image of the complexes
  Analysis of SNP data by mapping them onto 3D strucrure Protein 3D structure comparison
  Protein 3D structure prediction
  Protein sequence analysis against complete genomes
  

• Contact

  Graduate School of Information Science, Room A504
  Tel/Fax : +81-743-72-5396
  
  

• Curriculum Vitae
  • Year of Birth : 1967
  • March 1992 (Heisei 4): Bachelor's degree. Department of Precision Engineering, Faculty of Engineering, The University of Tokyo
  • March 1997(Heisei 9): Ph.D. Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Shimizu Lab
  • April 1997(Heisei 9): COE Research Fellow, National Institute of Genetics, Nishikawa Lab.
  • April 1999(Heisei 11): Postdoctoral Research Fellow, Japan Science and Technology Corporation, working in National Institute of Genetics, Nishikawa Lab.
  • July 2000 (Heisei 12) : Postdoctoral Research Fellow, Japan Society for the Promotion of Science, working in National Institute of Genetics, Nishikawa Lab.
  • October 2001 (Heisei 13) : Adjunct Associate Professor, NAIST Bioinformatics Unit
  • April 2006(Heisei 18)--March 2011 (Heisei 23): Associate Professor, Graduate School of Information Science, Nara Institute of Sciece and Technology

• Publications
  • Kawabata T. (2009). "Detection of multi-scale pockets on protein surfaces using mathematical morphology" Proteins, in press. [PubMed] [Link to GHECOM server]
  • Kawabata T. (2008). "Multiple subunit fitting into a low-resolution density map of a macromolecular complex using Gaussian mixture model". Biophysical Journal, 95,4643-4658. [PubMed]
  • Fukuhara N., Kawabata T. (2008). "HOMCOS: A server to predict interacting protein pairs and interacting sites by homology modeling of complex structures". Nucleic Acids Research, 36, Web server issue, W185-W189. [PubMed] [Nucl.Acids Res.]
  • Fukuhara N., Go N., Kawabata T. (2007). "Prediction of Interacting Proteins from Homology-modeled Complex Structures Using Sequence and Structure Scores", BIOPHYSICS, Vol.3, pp 13.
  • Kawabata T, Go N. (2007) "Detection of pockets on protein surfaces using small and large probe spheres to find putative ligand binding sites". Proteins, 68,516-529. [PubMed]
  • Uehara K, Kawabata T, Go N.(2004). "Filtering remote homologues using predicted structural information". Protein Eng Des Sel., 17, 565-570. [PubMed]
  • Kawabata,T. (2003) "MATRAS: A Program for Protein 3D Structure Comparison", Nucleic Acids Research, Vol. 31, pp. 3367-3369 [PubMed].
  • 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. [PubMed]
  • Kawabata,T. and Nishikawa,K. (2000) "Protein structure comparison using the Markov transition model of evolution," Proteins, Vol 41, pp. 108-122. [PubMed]
  • 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. [PubMed]
  • 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 [PubMed]
  • Kawabata, T. and Doi, J.(1997) "Improvement of Protein Secondary Structure Prediction Using Binary Word Encoding", Proteins, Vol 27, pp. 36-46. [PubMed]
• Publications (collaborative works)
  • Tsubota T, Tajima R, Ode K, Kubota H, Fukuhara N, Kawabata T, Maki S, Maki H. "Double-stranded DNA binding, an unusual property of DNA polymerase epsilon , promotes epigenetic silencing in Saccharomyces cerevisiae". J Biol Chem. 2006 Aug 16; [PubMed]
  • Ohta T, Kawabata T, Nishikawa K, Tani A, Kimbara K, Kawai F. "Analysis of amino acid residues involved in catalysis of polyethylene glycol dehydrogenase from Sphingopyxis terrae, using three-dimensional molecular modeling-based kinetic characterization of mutants". Appl Environ Microbiol. 2006 Jun;72(6):4388-96. [PubMed]

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