Journal of Computer Chemistry, Japan
Online ISSN : 1347-3824
Print ISSN : 1347-1767
ISSN-L : 1347-1767
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  • Ryo HATADA, Kouichiro KATO, Koji OKUWAKI, Kaori FUKUZAWA, Yuji MOCHIZU ...
    2020 Volume 19 Issue 1 Pages 1-7
    Published: 2020
    Released: June 10, 2020
    [Advance publication] Released: May 22, 2020
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    We have analyzed the interaction between calcite / hydroxyapatite and peptides by using the pair interaction energy decomposition (PIEDA) analysis of the fragment molecular orbital (FMO) method, based on interest in the biomineralizations. Furthermore, we have performed a multiple regression analysis using PIEDA results as well as structural data to clarify important factors of the interaction energies. As a result, it was found that "Interaction with short-range fragment" is an essential descriptor in the calcite system and also that "Distance between residue and surface of crystal" plays an important role in the hydroxyapatite system. This contrast reflects that the electrostatic interaction dominates in the former system but the charge-transfer has an additional effect in the latter.

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  • Kohei YAMATO, Hiroaki KATO, Tetsuo KATSURAGI, Yoshimasa TAKAHASHI
    2020 Volume 19 Issue 1 Pages 8-17
    Published: 2020
    Released: June 15, 2020
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    In this paper, we describe a multiple representation method of protein sequence motifs using sequence binary decision diagrams (SeqBDDs) and their application for motif search. A SeqBDD is a compressed representation of a set of sequences such as multiple strings. In this study, we developed two algorithms for SeqBDDs. The first is for constructing a SeqBDD which expresses amino acid sequences of the corresponding motifs, and the second is for building an automaton equivalent to a deterministic finite automaton for a SeqBDD by adding state transition to it. For the evaluation of their performances, we used our method to search for three highly conserved domains in the matrix metalloproteinase (MMP) family against all 555,594 amino acid sequences obtained from UniProtKB/Swiss-Prot (Release 2017_09) and compared results with the similar searches using PROSITE patterns. The methods showed better results on precision, recall and F-measure than those of using PROSITE patterns.

  • Makoto YABE, Kain CHIN, Kazuyoshi UEDA, Minoru TAKEDA
    2020 Volume 19 Issue 1 Pages 18-24
    Published: 2020
    Released: July 13, 2020
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    To perform molecular modeling or quantum chemistry calculations, a 3D file of a molecule of interest is required. The 3D file includes atomic types, coordinates, connectivity, and other structural data of a molecular model. A 3D file for a common molecule is available from existing data sources such as articles and databases in the web, or it can also be prepared using molecular modeling software. The use of computational chemistry techniques is expected to increase among researchers and students studying related subject matter if a molecular model built using a commercial molecular model kit can be directly subjected to computational analysis. Thus, we developed the Mm2cML software to facilitate the preparation of a 3D file from a real molecular model. Mm2cML is a web application based on structure from motion and multi-view stereo technologies in combination with a web interface. The effectiveness of the software was confirmed by evaluating the accuracy of vertical 3D models that were created using multiple 2D images. Further evaluation was performed through quantum chemistry calculations using 3D files obtained from vertical 3D models.

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