Journal of Computer Chemistry, Japan
Online ISSN : 1347-3824
Print ISSN : 1347-1767
ISSN-L : 1347-1767
Volume 17, Issue 4
Displaying 1-4 of 4 articles from this issue
Foreword
General Papers
  • Tetsuo KATSURAGI, Shigehiko KANAYA, Yoshimasa TAKAHASHI
    2018 Volume 17 Issue 4 Pages 163-171
    Published: 2018
    Released on J-STAGE: December 26, 2018
    Advance online publication: July 20, 2018
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    Structurally similar molecules often have similar properties. This also applies to their molecular frameworks and biological activities. In this study, we have developed a dictionary tool NTGdic/BOC (NTG dictionary for Bioactive Organic Compounds) which can be used to look up ring-based molecular frameworks referred to as NTG (Non-terminal vertex graph) and biological activities. We analyzed the chemical structures of 51,247 bioactive natural organic compounds taken from KNApSAcK Family database and extracted the NTGs of their molecular graphs. Totally 57,868 NTGs were extracted in five different graph expression levels such as simple graph, vertex-weighted graph, edge-weighted graph and so on. They were associated with 140 known biological activities. The NTG-activity dictionary was implemented as a relational database of the NTGdic/BOC. The dictionary tool allows us to search for NTGs and the relevant biological activities. It also allows similarity structure searching or similar NTG searching.

  • Eiji SHINSHO, Koji OKUWAKI, Hideo DOI, Yuji MOCHIZUKI, Takayuki FURUIS ...
    2018 Volume 17 Issue 4 Pages 172-179
    Published: 2018
    Released on J-STAGE: December 26, 2018
    Advance online publication: September 12, 2018
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    In order to perform efficient nanoparticle design in drug delivery systems, prediction of physical properties and elucidation of the molecular mechanism are expected by using molecular simulation. In this study, we investigated the molecular mechanism of lipid bilayer formation and mixed lipid vesicle formation using the dissipative particle dynamics (DPD) method and small angle X-ray scattering measurement. Parameters of inter-molecular interaction used for the DPD simulation were estimated in quantum mechanical level by the fragment molecular orbital method (FMO-DPD method). In lipid bilayer formation, it was found that the phospholipid having an unsaturated bond (DOPC) has higher membrane fluidity than the phospholipid (DPPC) having only saturated bonds. In the vesicle formation mixed with phospholipid and positively charged lipid, it was also found that as the proportion of positively charged lipid increases, the fluidity of the membrane increases and the shape changes from a sphere to a flat sphere.

  • Junko KAMBE, Yuji OBARA, Tomoo AOYAMA, Umpei NAGASHIMA
    2018 Volume 17 Issue 4 Pages 180-187
    Published: 2018
    Released on J-STAGE: December 26, 2018
    Advance online publication: November 30, 2018
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    A method for analysis of satellite image in visible light was developed for making a document and teaching material of new environmental science. Since environmental contamination manifests especially in fine hue changes, we newly developed a hue and contrast emphasis method of satellite image. We investigated the satellite photograph by Himawari No. 8 taken after the sinking accident of Tanker Sanchi in January 2018. As a result, we could not find the influence of condensate dumped into the sea, it is found that there is a possible sea surface black band. It was also found that the eutrophication of the East China Sea extends near the Japanese exclusive economic zone (Exclusive Economic Zone, EEZ), sometimes the polluted seawater reaches the western coast of Kyushu island.

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