Chem-Bio Informatics Journal
Online ISSN : 1347-0442
Print ISSN : 1347-6297
ISSN-L : 1347-0442
Volume 6, Issue 1
Displaying 1-2 of 2 articles from this issue
Original
  • Ganga D. Ghimire, Kenichiro Imai, Fumitsugu Akazawa, Toshiyuki Tsuji, ...
    2006 Volume 6 Issue 1 Pages 1-16
    Published: 2006
    Released on J-STAGE: May 19, 2006
    JOURNAL FREE ACCESS
    A G-protein binds to a G-protein-coupled-receptor (GPCR) by physical interactions between the amino acid sequences. Various physical properties of possible binding regions at the C- and N-termini of α subunits of G-proteins were analyzed in order to classify the four families of α subunits, α s, α i/o, α q/11 and α 12/13, as well as the eight subfamilies. The distribution of the charge density and the hydrophobicity of 100 residues at the C-terminus enabled discrimination of the four families of α subunits, whereas the same physical properties of 60 residues at the N-terminus enabled discrimination of the subfamilies.
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  • Motoi Tobita, Ken Horiuchi, Kenji Araki, Masashi Nemoto, Hiroyasu Shim ...
    2006 Volume 6 Issue 1 Pages 17-28
    Published: 2006
    Released on J-STAGE: May 19, 2006
    JOURNAL FREE ACCESS
    A data-matrix viewer, BirdsAnts, is developed for the effective visualization of large scale protein-small molecule interaction data. One of two design concepts is the simultaneous visualization of three kinds of data: data pertaining to proteins, those to small-molecules, and those to interactions between them. The other is switching of global and local views of data back and forth. To evaluate BirdsAnts, a data-matrix was generated by processing a protein-small molecule interaction database. Analyzing the matrix, two known facts were rediscovered. First rediscovery was the knowledge that each function of vitamin B12 is exercised by interaction to a different protein. Second was that cyclooxygenase inhibitors were correctly classified into known classes by two-step clustering calculations. The results of the evaluation show that BirdsAnts has future potential for the effective visualization of protein-small molecule interaction data.
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