Journal of Computer Aided Chemistry
Online ISSN : 1345-8647
ISSN-L : 1345-8647
Volume 7
Showing 1-22 articles out of 22 articles from the selected issue
  • Hitoshi Iwamoto, Hidefumi Sakamoto, Keiichi Kimura
    2006 Volume 7 Pages 1-9
    Published: 2006
    Released: February 28, 2006
    JOURNALS FREE ACCESS
    Metal ion extractability in liquid-liquid extraction using spirobenzopyrans possessing a crown ether moiety was evaluated by molecular dynamics. It was found that a longer alkyl group attached to the spirobenzopyran ring results in greater stability in the organic phase. The same trend was observed for the model metal complex. When the crowned spirobenzopyran was complexed with an alkali metal ion, the steric energy in the aqueous phase was decreased. However, the energy was higher than that of the complex in the organic phase; as a result, the complex was more stable in the organic phase. In addition, the metal ion which forms the most stable complex depends on the ring size of the crown ether. The tendency was confirmed by the liquid-liquid extraction of alkali metal ion with the crowned spirobenzopyran. This indicates that it is possible to predict the properties of extraction reagents from their steric energy values calculated using molecular dynamics.
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  • Satoshi Kawamura, Masamoto Arakawa, Kimito Funatsu
    2006 Volume 7 Pages 10-17
    Published: 2006
    Released: March 03, 2006
    JOURNALS FREE ACCESS
    We propose the GAWLS (Genetic Algorithm-based WaveLength Selection) method as a new variable selection technique for spectrum data. It is technique to choose wavelength with important information by a region unit. In this study, we analyzed a NIR spectrum data in precision agriculture with the GAWLS method and confirmed its utility. Q2 of the GAWLS model was 0.732 and we discovered 3 regions related to quantity of water in the soil. It is expected that we will be able to make stable model with high predictive accuracy by using the GAWLS method, and discovery of informative regions and chemical attribution of constructed model becomes easy.
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  • Hiroshi Yamamoto
    2006 Volume 7 Pages 18-30
    Published: 2006
    Released: March 24, 2006
    JOURNALS FREE ACCESS
    The equations for obtaining the viscosity and melting points of ionic liquids were built. These euations could be applied Imidazolium, pyridinium or ammonium cation with some kind of anion. Molecular descriptors for predicting viscosity of these ionic liquids were based on the size and electrostatic properties in the cations. For the melting points, hydrogen bonding force evaluation became important. To determine coefficients in none linear equation, Genetic Algorithm(GA) were adapted. Eight-parameter correlation was obtained for viscosity with R2=0.9464. But melting point correlation was hard to converge especially with BF4 anion salts. So individual equation was built for BF4 anion. Ten-parameter correlation was obtained for melting point with R2=0.837. Experimental melting point itself varied widely, so this squared correlation coefficient is correct enough.
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  • Toshiyuki Mitsui, Minesada Hida
    2006 Volume 7 Pages 31-37
    Published: 2006
    Released: March 24, 2006
    JOURNALS FREE ACCESS
    The biochemistry sample extracted from the criminal spot may have received change by decomposition etc. An exact conclusion is not obtained from the result analyzed using such a sample, and may draw the mistaken conclusion from it. In order to avoid such a thing, it is necessary to investigate that whether a sample can use it for analysis
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  • Hiroko Satoh, Tomoo Nukada, Katsuhito Akahane, Makoto Sato
    2006 Volume 7 Pages 38-47
    Published: 2006
    Released: June 23, 2006
    JOURNALS FREE ACCESS
    The goal of our project is to develop basic systems for a new type of chemical educational system by using a haptic device to virtually feel attractive and repulsive force in van der Waals molecular interaction. We focus on the interaction between rare-gas atoms (He, Ne, Ar, Kr, and Xe) and construct a robust and basic system. Two visually different systems are developed. One is E-HaptiChem, which uses a 3D-multimedia open-source graphics library, JUN, as a general basis, and uses a chemical open-source graphics library, ChemoJun, as a chemical tool. The other system is AVS-VI, which uses an AVS graphics library. In the current phase, basic functions have been developed and implemented in both systems. This paper outlines the project, the methods, and the first results of our efforts in determining the basic requirements for the molecular haptic system.
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  • Harumi Matsui, Yuko Ishiwaka, Jyunya Kobayashi, Osamu Konishi
    2006 Volume 7 Pages 48-56
    Published: 2006
    Released: July 14, 2006
    JOURNALS FREE ACCESS
    An immune algorithm (IA), which is a heuristic method for selection, was used to optimize compositions of the Cu/Al2O3 catalyst for the methanol steam-reforming reaction. An artificial neural network (ANN) that was trained on observed data was adopted to evaluate the catalytic activity in an immune algorithm. After 10,000 generations, we obtained several candidate catalysts. Compared with the results of a genetic algorithm (GA) for the same evaluation function, the results of an IA presented potentially useful candidate catalysts. During initial stages of developing catalysts, extensive screening using search methods, such as immune algorithms, should prove effective.
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  • Hidetoshi Maruyama, Kenji Kaijiri
    2006 Volume 7 Pages 57-68
    Published: 2006
    Released: July 19, 2006
    JOURNALS FREE ACCESS
    In the former work, we proposed a novel 3D protein structural homology search algorithm based on the Triangle ID comparison method. In that work, we focused a triangle structure consisting of three amino acids and called it as Triangle ID. We assumed that proteins can be characterized by using these Triangle IDs. To prove the validness of this assumption, we developed the homology search tool, did several experiment based on the sample data sets, and showed the validness of our assumption and the scalability of our method. On the other hand, identification of 3D characteristics of protein is required, and we assumed that our Triangle ID method can be used for this purpose. In this study, we propose 3D protein structure clustering by using 3D motifs based on the Triangle ID. The 3D motifs were extracted from the common Triangle IDs which have the same feature and belong to the same protein families. We defined the selectivity criteria, did several experiments, and showed the effectiveness of our proposed approach. We selected protease families as our experiment target, because they are attracted the attention as drug target proteins. Our method opens the possibility of the efficient protein function analysis by 3D motifs based on the Triangle ID.
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  • Uemura Keisuke, Masamoto Arakawa, Kimito Funatsu
    2006 Volume 7 Pages 69-77
    Published: 2006
    Released: July 28, 2006
    JOURNALS FREE ACCESS
    We have developed a novel chemoinformatics approach to propose new catalyst. Regression models to predict conversion and selectivity from catalyst compositions, temperature, pressure, etc. are built by using PLS(partial least squares) method. These models are used for searching compositions of catalysts that are expected to be efficient. Multiobjective optimization of conversion and selectivity by use of Pareto optimum makes it possible to choose a suitable catalyst for required catalytic performance. We collected catalytic data about direct epoxidation of propylene from patents and have applied the approach to them. The results showed that our approach is effective in catalyst design.
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  • Shingo Iwabuchi, Shinsaku Kozakai, Noriyuki Kurita
    2006 Volume 7 Pages 78-86
    Published: 2006
    Released: September 20, 2006
    JOURNALS FREE ACCESS
    Calcium ion (Ca) plays many essential roles as an intercellular messenger in the living body. The binding of Ca to the calcium binding protein (CaBP) is concerned with the mechanism of messenger passing. In the present study, we investigated the stable structures and their electronic properties for three types of CaBPs having EF-hand motif, using molecular simulations based on classic molecular mechanics and semiempirical molecular orbital methods. Furthermore, the effect of Ca binding to CaBP was investigated to elucidate the difference in Ca binding affinity between the CaBPs. The results clarified that the difference in Ca binding affinity of CaBPs is explained by the binding energies between CaBP and Ca.
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  • Naoto Tanaka, Takashi Abe, Satoru Miyazaki, Hideaki Sugawara
    2006 Volume 7 Pages 87-93
    Published: 2006
    Released: September 15, 2006
    JOURNALS FREE ACCESS
    We have developed the G-InforBIO for seamless integration of browse and analysis of genomic data. Major functions of the suite are database management, data retrieval, sequence data analysis and the visualization for genomics. An annotation database accommodates multiple flat files (FFs) of entries registered in the International Nucleotide Sequence Database Collaboration (INSDC, DDBJ/EMBL/GenBank) and also tab-delimited files of local data. Genome information on the imported annotation database can be readily retrievable using keyword searches. A subset of nucleotide and protein sequences can be also retrieved for the further analysis and graphical representation. The G-InforBIO includes sequence analysis programs for cluster analysis (BLASTCLUST, ClustalW, and SOM) and homology analysis (MegaBLAST, BLAST, Blat, and Sim4). The analysis can be applied to the retrieved subset and data imported from outside. The system provides a broad-ranging utilization of genome information. The suite is written in Java so that it is executable in Macintosh OSX, Windows XP, Linux, and Unix machines and will be downloadable from http://www.wdcm.org/inforbio/G-InforBIO/download.html. The instruction manual of the G-InforBIO can be browsed at http://www.wdcm.org/inforbio/G-InforBIO/manual_E/index.htm.
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  • Yoko Shinbo, Shun-ichi Sakaguchi, Yukiko Nakamura, Md. Altaf-Ul-Amin, ...
    2006 Volume 7 Pages 94-101
    Published: 2006
    Released: September 15, 2006
    JOURNALS FREE ACCESS
    Secondary metabolites are highly species specific and play a role for the survival of the producing organism within its natural habitat. Several databases have been made by collecting metabolite information of various organisms, and they provide some chemical information and biological pathways on metabolites, however, they don't provide the relationships between metabolites and their biological origins. To systematically and comprehensively understand species-specific diversity of metabolites, we have designed a database system called KNApSAcK. This system is useful for obtaining information on metabolites and their corresponding species, chemical structure and biological activity. The database has a tool that can be used for analyzing datasets acquired using Fourier transform ion cyclotron mass spectrometry (FT/ICR-MS). We collected information on 25,930 metabolite-species pairs encompassing 11,075 metabolites and 8,557 species from published references (January 19th, 2006). This database system and online manual are freely available at http://kanaya.naist.jp/KNApSAcK/. This database system is available in two different versions, Web-version and Download-version. If you want to use the Download-version, at the beginning, you have to install KNApSAcK and Java 1.4.2 on your local computer. The Download-version has been coded in Java.
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  • Akira Ohyama, Ken Kurokawa, Kyotetsu Enai, Hitohiro Saitoh, Shigehiko ...
    2006 Volume 7 Pages 102-115
    Published: 2006
    Released: September 15, 2006
    JOURNALS FREE ACCESS
    We are making an attempt to perform the molecular biological experiments in silico, one of the most promising alternative means of the biological experiments in vitro. Among the various fields of experiments, this paper is especially focused on molecular cloning, because DNA information is more systematically and exhaustively collected than that of other molecules. There are some advantages in in silico experiments in view of planning molecular biological experiments, usage as lab notebook, educational tool to learn molecular biological experiments. However, performing in silico cloning requires some formulations such as recording of the end shapes of digested products by restriction enzymes or amplified products by PCR. For this purpose, we introduce some extensions to GenBank/EMBL database annotation convention, and incorporate them into existing convention as new feature keys and qualifiers. In addition, features on a DNA sequence are occasionally truncated in the case of amplified products of PCR or digested fragments by restriction enzymes, therefore the annotations about the truncated features should be also formulated. The ambivalent nature of DNA requires frequent changes of the interested strand to and fro, therefore a reverse complementary operation of large size DNA is necessary to be implemented for such software. According to these definitions or data descriptions, we have developed a software tool for in silico experiments, named in silico MolecularCloning, and perform a few of typical molecular cloning experiments on computer, and verified that this approach would be effective.
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  • Makoto Kinouchi, Ken Kurokawa
    2006 Volume 7 Pages 116-124
    Published: 2006
    Released: September 15, 2006
    JOURNALS FREE ACCESS
    Over 250 bacterial genome sequences have been completely determined. This makes it possible to study the species-specific gene expression systems involving transcription and translation for a wide range of organisms. To understand species-specific translation system, it is important to comprehend the whole set of tRNAs for individual species. When we could comprehend the whole set of tRNAs for individual speices, we could estimate optimal codons for individual species based on levels of tRNAs and multivariate analysis of codon usage for individual species because of the high correlation between tRNA contents and copy numbers of isoaccepting tRNA genes in genomes. Thus, the copy numbers of isoaccepting tRNAs in genomes are very important for understanding species-specific translation system. In the present study, we developed new identification package of tRNAs from a DNA sequence called tRNAfinder. The procedure for detecting tRNAs are as follows: Firstly, tRNA candidates are detected based on tRNA cloverleaf secondary structure. Secondly, tRNAs are selected from the candidates based on the consensus rules derived from real tRNAs. In the present study we illustrate tRNAfinder algorithm and the performance of the present system by comparing composition of tRNAs from publicly available web sites using 72 gamma-proteobacteria. Furthermore we examine the universal system of tRNA composition in gamma proteobacteria. The programs developed in the present study are downloadable from our web site.
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  • Mitsuru Yano, Shigehiko Kanaya, Md. Altaf-Ul-Amin, Ken Kurokawa, Masa ...
    2006 Volume 7 Pages 125-136
    Published: 2006
    Released: September 15, 2006
    JOURNALS FREE ACCESS
    With the recent advances of sophisticated bioinformatics tools and analytical technology, the systems biological approach becomes more realistic to solve biological problems. The aim of this study is to illustrate a feasibility of batch-learning self-organizing map (BL-SOM) for high-throughput analysis of post-genomic data on plant biology. BL-SOM is a modification of the conventional SOM, which provides colored feature maps independent of the order of data input. We conducted the nutritional stress experiments on a model plant Arabidopsis thaliana and applied the BL-SOM to analysis of the data sets of metabolome and transcriptome obtained by Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICRMS) and DNA microarray. BL-SOM analyses of non-targeted metabolome data provided metabolic fingerprinting of global responses to nutritional stress and developments. Using the clustering performance of BL-SOM, we deduced metabolite identification from accurate mass values and elucidated a metabolic mechanism responding to sulfur deficiency. Transcriptome data were also analyzed by BL-SOM, and genes responding to sulfur deficiency were classified according to their expression patterns. The result showed that functionally related genes were clustered in the same or neighbor lattice points. We examined each cluster and deduced putative functions of genes involved in glucosinolate biosynthesis, and the function of some of those genes was identified by biochemical experiments. Our present study suggests that application of BL-SOM to an integrated post-genomic omics data gives great possibilities for more accurate prediction in systems biology. The BL-SOM software is provided freely at our web site (http://prime.psc.riken.jp).
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  • Tatsunari Nishi, Yasushi Masuda, Yoshifumi Ujiie, Naoki Morita, Masahi ...
    2006 Volume 7 Pages 137-140
    Published: 2006
    Released: September 15, 2006
    JOURNALS FREE ACCESS
    The GeneLook web server (http://www.genaris.co.jp/plaza/) provides an interface to an ab initio prokaryotic gene identification program, GeneLook. The GeneLook predicts protein-coding sequences (CDSs) with high accuracy with no prior knowledge of the sequence composition. The GeneLook identifies CDSs even from a short DNA sequence, but its length is recommended to be more than 10 kb to obtain satisfactory prediction results.
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  • Hiroko Satoh, Atsushi Aoki, Hiroko Asaoka
    2006 Volume 7 Pages 141-149
    Published: 2006
    Released: September 15, 2006
    JOURNALS FREE ACCESS
    ChemoJun, a new open source graphics library for chemical visualization, has been developed and opened to the public. The purpose of the ChemoJun project is to develop a basic technology of chemical software. ChemoJun consists of several basic modules for visualizing chemical information, these modules are used in developing graphical user-interface programs of chemical software, including systems for characterizing and predicting chemical reactivity and for predicting NMR chemical shift values. This paper outlines the ChemoJun project and describes the latest version, 050.
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  • Md. Altaf-Ul Amin, Hisashi Tsuji, Ken Kurokawa, Hiroko Asahi, Yoko Shi ...
    2006 Volume 7 Pages 150-156
    Published: 2006
    Released: September 15, 2006
    JOURNALS FREE ACCESS
    In this paper we present a graph clustering software, which we have developed based on a clustering algorithm we published previously. The algorithm tends to isolate densely connected regions of a graph as clusters. Users have freedom to choose two input parameters within reasonable range and thus to affect the outcome of the clustering up to certain extent. Though this software can be used for graph clustering in general but it mainly focuses on detection of protein complexes in interaction networks. The proposed software makes it possible to detect and visualize clusters of proteins in interaction networks which mostly represent molecular biological functional units. We believe that the present software can be applied not only to other biological networks but also to networks in many other applications where finding cohesive group is an agenda.
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  • Takeshi Tomiki, Tamio Saito, Masashi Ueki, Hideaki Konno, Takeo Asaoka ...
    2006 Volume 7 Pages 157-162
    Published: 2006
    Released: September 15, 2006
    JOURNALS FREE ACCESS
    We have constructed a natural products database, "RIKEN Natural Products Encyclopedia (RIKEN NPEdia)", as an informatics part of chemical resource bank, "the RIKEN Natural Products Depository (RIKEN NPDepo)". Approximately 25,000 compound data are now listed in NPEdia, some of which were transferred from "KNApSAcK", a secondary metabolites database constructed by Prof. Kanaya and his colleagues (http://kanaya.aist-nara.ac.jp/KNApSAcK/, http://prime.psc.riken.jp/ (mirror site)). Compounds listed in NPEdia are mainly secondary metabolites isolated from actinomycetes, fungi, plants and other organisms. Each compound data consists of molecular structure, origin, and physico-chemical and biological properties. MOL files can be also downloaded. Ultra-Violet, MS/MS and NMR spectra will also be included in the near future. This database involves three functions: (1) searching for compounds, (2) registering compound data and (3) co-operating in compound-order system. We are now trying to integrate metabolites with metabolic pathway maps, protein-protein interaction maps, and chemical genomics maps (relationship between metabolic pathways and small molecules "bioprobes" interacting them). We think NPEdia should be a useful database friendly to researchers in various research fields. The details and latest news about NPEdia are described on the website (http://npd.riken.jp/).
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  • Hirofumi Nonaka, Hideo Sekino
    2006 Volume 7 Pages 163-167
    Published: 2006
    Released: November 09, 2006
    JOURNALS FREE ACCESS
    For prediction of molecular property and elucidation of physical mechanism it is important to use molecular dynamics(MD) simulation. However, there is necessity for speeding up MD simulation because these simulations of large size molecules such as dendrimer expend huge calculation cost. For that purpose, it is most effective to improve the part for calculating Coulomb interactions which dominates in the entire simulation process. The mutipole algorism ,which has same effect as converting far many particles to pseudo one particle, is one of the most powerful methods for solving the problem. In this research, we develop and improve the Multipole method for MD simulation. The Fast Multipole Method(FMM), which is one of the Multipole algorisms, is often used in the MD simulation. The drawback of this method is the high cost of the improvement in the accuracy. In this research, we develop a new FMM. For improving the accuracy efficiently, we employed the least mean square method on the FMM local expansion, instead of Taylor expansion. In order to compare our FMM with conventional FMM, we calculate Coulomb energy among the particles generated at random and that among electronic charges of fifth generation dendrimer. It is shown that the accuracy of our FMM is twice as much as that of the conventional method under the same condition, and that the calculation cost of our FMM is almost equivalent to the conventional FMM.
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  • Hiroshi Yamamoto, Katsumi Tochigi
    2006 Volume 7 Pages 168-177
    Published: 2006
    Released: November 09, 2006
    JOURNALS FREE ACCESS
    The chlorofluorocarbon has been used for foaming agents because of its low thermal conductivity. Research Institute of Innovative Technology for the Earth (RITE) examined the replacements which does not include chlorine. Hydro-fluoro-ethers (HFEs) and hydro-fluoro-ketones (HFKs) were synthesized, and the thermal properties were measured. The thermal conductivity of gas was measured, and it was summarized in a database. We built estimation equation of a gas thermal conductivity of organic compounds that can use from CFC to normal hydrocarbon compound. We used polynomial expansion type of estimation equation and decided the coefficients with genetic algorithm. From cross-validation result, our polynomial expansion type of estimation equation predicted the thermal conductivity of gas with correlative coefficient R2=0.996. We also showed that we could design structure to make thermal conductivity small when we used this estimation equation reversely.
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  • Kiyokazu Takahashi, Noriyuki Kurita
    2006 Volume 7 Pages 178-189
    Published: 2006
    Released: November 23, 2006
    JOURNALS FREE ACCESS
    We investigated the stable structures and their electronic properties of ATP, ADP, AMP and GTP by ab initio molecular orbital calculations based on density functional theory. Furthermore, stable structures and electronic properties of Mg2+ complexes (Mg-ATP, Mg-ADP, Mg-AMP and Mg-GTP) were investigated to elucidate that Mg-ATP is more reactive and that hydrolysis reaction can take place at the terminal P atom.
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  • Effect of Water Molecules on HOMO Distribution of DNA
    Takayuki Tsukamoto, Yasuyuki Ishikawa, Takayuki Natsume, Kenichi Dedac ...
    2006 Volume 7 Pages 190-200
    Published: 2006
    Released: November 23, 2006
    JOURNALS FREE ACCESS
    To elucidate the effect of hydration on the electronic properties of duplex DNA, we investigated the electronic properties of both dry and hydrated DNA duplexes having stacked 10 base-pairs by density functional molecular orbital (MO) calculations. The water molecules bound to the minor groove of DNA were found to contribute to the MO distributions around the HOMO, indicating the possibility that these water molecules can be directly involved in the process of hole transfer through DNA. On the other hand, the water molecules bound to the backbones of DNA have no remarkable effect on the MO distributions around HOMO.
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