Journal of Chemical Software
Online ISSN : 1883-8359
Print ISSN : 0918-0761
ISSN-L : 0918-0761
Volume 7 , Issue 3
Showing 1-5 articles out of 5 articles from the selected issue
Original Papers
  • Susumu NARITA, Tetsuo MORIKAWA, Tai-ichi SHIBUYA
    2001 Volume 7 Issue 3 Pages 99-102
    Published: September 01, 2001
    Released: February 28, 2002
    A computer program written in the Fortran 77 language is given, which enumerates Kekulé structures in fullerene molecules. It is easy to compute the Pauling bond order for each bond of the fullerene molecules by means of the program because the new algorithm is applicable to substructures in the molecules.
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  • Eiichi AKAHO, Garret MORRIS, David GOODSELL, David WONG, Arthur OLSON
    2001 Volume 7 Issue 3 Pages 103-114
    Published: September 15, 2001
    Released: February 28, 2002
    The capability to propose feasible ways of binding a putative ligand inhibitor to a known receptor site is crucial to the successful structure-based drug design. A computer docking approach is to position or “dock" ligand and receptor molecules together in many different ways and then score each orientation by applying a reasonable evaluation function. AutoDock3.0 is an unbiased type docking program in which a user does not have to direct a ligand to an active site, but the system finds an optimal position after a ligand is placed in a random manner. Synthesized derivatives of the intact inhibitor (inh1) of HIV protease were investigated for their docking modes as compared with their Ki values. Among the derivatives, inh3trans and inh6H were found to be more powerful inhibitors of HIV protease than the others. Gibbs free energy calculated by applying molecular mechanics interaction energies was compared with the one obtained by using experimental inhibitory potencies for a series of HIV protease inhibitors, and a fairly good correlation was found between the two. Based on this favorable correlationship between the computational and the experimental results, the computational experiments were pursued for the compounds drawn by Sybyl taking into consideration the fact that unexploited carbon affinity regions (or hydrophobic regions) with sizable volume were detected on the docking study of inh1 and inh8 against HIV protease. Those were compounds with a t-butyl substituted by various hydrophobic side chains. Among those a compound with a benzyl group exhibited the lowest docking energy. Since one of the goals of this paper was to perform the computational drug-design experiment to investigate potential HIV protease inhibitors, the authors would like to leave the clinical investigational work for the expertise of those areas.
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  • Tomoko FUKUDA, Sumie TAJIMA, Hisato SAITOH, Umpei NAGASHIMA, Haruo HOS ...
    2001 Volume 7 Issue 3 Pages 115-128
    Published: September 15, 2001
    Released: February 28, 2002
    We present a method to estimate elution induced time and 80% elution time of polymer-coated manure using 1/f fluctuation analysis of near-infrared reflection spectrum and a perceptron type neural network and/or Ck interpolation scheme in order to reduce the evaluation time of elution induce time and 80% elution time. Usually, the evaluation time of elution induce time and elution speed is more than 20 days.
    In the case of the neural network, relative error is almost less than 10%. Furthermore, the slopes of regression lines for the correlation between observed and calculated values are almost 0.9. For the Ck interpolation scheme, the error is a little bit larger than those of the neural network but less than 20%. This method is applicable for actual use because more than 10% error is included in the observed values. This method requires almost 10 minutes so that the evaluation cost of elution induce time and elution speed of polymer-coated manure will be significantly improved.
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  • Yoshimichi OIKAWA, Jiro TAKANO, Shunmei MITSUZAWA
    2001 Volume 7 Issue 3 Pages 129-138
    Published: September 15, 2001
    Released: February 28, 2002
    A multimedia CAI software is a useful material for chemical education. The information content of it is enormous. The software must be provided with a CD-ROM for each student or must be set up on each computer, in case many students use it individually.
    Our multimedia CAI software available on the World Wide Web (WWW) will be managed on only one computer that is networked to the Internet. Students will access to this software from each computer every time that one can show information on the WWW.
    A diagram of the system is shown in Figure 1. The server consists of WWW-server program, database gateway, user database, HTML contents, streaming-type CAI software and other object files. This database gateway gives an easy way to control the database from HTML. A personal computer (PC) configuration of our use in a test and the classroom are shown in Table 1.
    When students access the server from each client-PC via WWW browser, the Log-in screen appears (Figure 2). They will select content from the Menu screen (Figure 3) after user-identification is successful. With our CAI software, they will be able to learn about acids and bases and how to do an acid-base titration (Figures 4 -8). The software contains several graphics and digital video source. The information content of the software is about 3 Mbytes.
    When server and clients-PC are connected to the same HUB, no difference in starting time is detected by 3 access types (Table 2). In a rush test of the system in the same situation as the class lecture, the starting time of the software increased with the number of clients (Table 3). The starting time of the software accessing to the server by under 10 clients is shorter than one at the same time using many clients.
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Technical Report