Doctor thesis

Naoshi Fukuhara "Prediction of Protein-Protein Interaction Using Homology-modeled Complex Structure". June,2007.

Reviewed Paper

• 2010

  • Kawabata T. 2010. "Detection of multi-scale pockets on protein surfaces using mathematical morphology" Proteins, 78, 1195-1211 [PubMed] [Link to GHECOM server]

• 2008
  • 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]
    Cover of Biophysical Journal is the model generated by us. [larger figure] [another figure]

  • Fukuhara N., Kawabata T. "HOMCOS: A server to predict interacting protein pairs and interacting sites by homology modeling of complex structures". Nucleic Acids Research, Web server issue, in press. [PubMed] [Nucl.Acids Res.] [Link to HOMCOS server]

• 2007
  • Fukuhara N., Go N., Kawabata T. "Prediction of Interacting Proteins from Homology-modeled Complex Structures Using Sequence and Structure Scores", BIOPHYSICS, Vol.3 (2007), pp 13.

  • Kawabata T, Go N. "Detection of pockets on protein surfaces using small and large probe spheres to find putative ligand binding sites". Proteins, 68, 516-529, (2007). [PubMed]

• 2006
  • 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]

    Cover of J.Biol.Chem. is the structure of DNA and proteins modeled by us. [image 900x1100] [image 2700x3300]

  • 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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