月別: 2018年4月

[Published online Journal of Computer Chemistry, Japan Vol.16, 167-169, by J-STAGE]
<Title:> クラスターの単純さに注目したデータ クラスタリングの高精度化とそのケモインフォマティクスへの応用
<Author(s):> 天野　晃, 山之内　昭博, 杉本　学, 和田　匡路
<Corresponding author E-Mill:> amano.kou(at)nims.go.jp
<Abstract:> A cluster validity index (CVI) called “simplicity index” (SI) is newly proposed to enhance the accuracy of data clustering in machine learning. This index is derived to emphasize the importance of simplicity in cluster structures. The characteristics ofSI and its advantages over the known methods in the literature are discussed. SI is applied to classification of nucleotide sequences of nitrogen-fixing genes.
<Keywords:> non-hierarchical clustering, clustering validity index
<URL:> https://www.jstage.jst.go.jp/article/jccj/16/5/16_2017-0062/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.16, 165-166, by J-STAGE]
<Title:> 天然ゴムの生合成過程解析
<Author(s):> 慶野　達也, 内田　希, 河原　成元, 秋山　和輝
<Corresponding author E-Mill:> tatsuya_keino(at)mst.nagaokaut.ac.jp
<Abstract:> Natural rubber is an excellent material in elasticity and abrasion resistance. However, the detailed structure of natural rubber is still unclear. We aimed to conduct conformational search and structural analysis using computational chemistry and to elucidate the biosynthetic process of natural rubber. From the calculation results, it was found that the structure is likely to have a rounded structure due to the intramolecular and intermolecular interaction that the terminal phosphate group gives to the polyisoprene moiety as a polar group, and both ends are fixed on the particle surface and become stable.
<Keywords:> Natural rubber, Molecular mechanics, CONFLEX, Molecuar dynamics, LAMMPS, Phosphate group
<URL:> https://www.jstage.jst.go.jp/article/jccj/16/5/16_2017-0059/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.16, 160-162, by J-STAGE]
<Title:> 分子動力学を用いたニューロプシンのペプチド認識に関する研究
<Author(s):> リントゥルオト　正美, 堀岡　洋太, 阿部　光将, リントゥルオト　ユハ
<Abstract:> The substrate specificity and selectivity on the chymotrypsin-type serine protease, neuropsin was investigated by using molecular dynamic simulation. The amino acid residues at l1 and l5, which are located adjacent to the neighboring residues of cleave site Argl3 on both sides, play important roles, and the interactions between these amino residues of peptide and loops D and H of protein regulate the affinity and catalytic activity.
<Keywords:>
<URL:> https://www.jstage.jst.go.jp/article/jccj/16/5/16_2017-0053/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.16, 163-164, by J-STAGE]
<Title:> 自動反応経路探索を用いる不斉触媒反応の機構解明と機械学習による効率的解析
<Author(s):> 畑中　美穂
<Corresponding author E-Mill:> hatanaka(at)ms.naist.jp
<Abstract:> The mechanism of enantioselectivity of the asymmetric aldol reaction catalyzed by Zn (II) complex was discussed based on the transition states (TSs) of the stereo-determining C-C bond formation step. To gather the TSs of the stereo-determining step exhaustively, an automated reaction path search method, called the artificial force induced reaction (AFIR) method, was applied. Though the obtained TSs reproduced the stereoselective ratio, it was difficult to extract the key information for the enantioselectivity. To analyze such TS structures efficiently, the automated clustering of the TSs by using the K-Means++ method, which was one of the unsupervised learning methods, was helpful.
<Keywords:> Asymmetric reaction, Chiral catalyst, Global Reaction Route Mapping (GRRM), Density functional theory (DFT), Unsupervised learning
<URL:> https://www.jstage.jst.go.jp/article/jccj/16/5/16_2017-0065/_article/-char/ja/