月別: 2021年12月

[Published online Journal of Computer Chemistry, Japan Vol.20, 106-111, by J-STAGE]
<Title:> 機械学習QSARの整数計画法に基づく逆解析法
<Author(s):> 仁 永持, 見深 朱, Naveed Ahmed AZAM, 和也 原口, 亮 趙, 達也 阿久津
<Corresponding author E-Mill:> nag(at)amp.i.kyoto-u.ac.jp
<Abstract:> We have developed a novel framework for inferring a chemical graph. Given an ANN that maps a feature vector x = f ( G ) of a chemical graph G to a predicted value η ( x ) of a chemical property to G, we formulate an integer program that simulates the functions f and η. Given a target value y*, we can infer a chemical graph G such that η ( f ( G ) ) = y * by solving the integer program.
<Keywords:> Machine learning, Integer programming, Chemical graphs, QSAR/QSPR, Molecular design
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/3/20_2021-0030/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, 112-115, by J-STAGE]
<Title:> 数学・数理科学からのアプローチによる分子動力学計算
<Author(s):> 深作　亮也, 溝口　佳寛, 檜貝　信一
<Corresponding author E-Mill:> higai(at)ark-i.com
<Abstract:> In the present report, we introduce our new three approaches based on the mathematics / mathematical sciences to the classical molecular dynamics calculations; 1) the approach by the analytical mechanics instead of the classical mechanics; 2) the approach to the periodic boundary condition by the torus model; 3) the approach by the mathematics-based programming substituting for the procedural (imperative) programming. Then, we found that these approaches are very effective to make calculations simpler, more compact, steadier, and firmer. Thus, it was concluded that the mathematical / mathematical scientific approaches are the promising ones to overcome various problems that we confront in the computational chemistry.
<Keywords:> Analytical mechanics, Periodic boundary condition, Torus model, Mathematics-based programming, Molecular dynamics calculations
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/3/20_2021-0043/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, 116-118, by J-STAGE]
<Title:> デジタルアニーラ前処理空間探索と拡張アンサンブル法による環状ペプチド分子の高速安定構造探索
<Author(s):> 谷田　義明, 佐藤　博之, 眞鍋　敏夫, 島　千絵子
<Corresponding author E-Mill:> tanida.yoshiaki(at)fujitsu.com
<Abstract:> Cyclization generally stabilizes the bioactive conformation of the peptide and increases its affinity for the target. However, since cyclic peptides frequently adopt multiple conformations in solution, the structural information is not fully understood in experiments, and the relationship between structure and function is not well understood. We demonstrate the practical possibilities of using a combination of a special purpose computing engine (Digital Annealer) and REST2 (replica exchange with solute tempering) simulation in “ab initio” structure prediction of macrocyclic peptides.
<Keywords:> Macrocyclic peptide, Digital Annealer, Lattice protein model, REST2, Structure prediction, Cluster analysis
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/3/20_2021-0036/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, 119-122, by J-STAGE]
<Title:> DSSC用のトリフェニルアミンドナーベース有機色素におけるベンゾチアジアゾールを補助置換基とした時の効果の解析
<Author(s):> 山崎　直人, 野村　泰志, 森川　大
<Corresponding author E-Mill:> nomuray(at)shinshu-u.ac.jp
<Abstract:> It has been reported that the introduction of a 2, 1, 3-benzothiadiazole (BTD) into an organic dye used in dye sensitized solar cells (DSSC) makes its conversion efficiency improve. In this study, we examine the effects of BTD’s from viewpoints of its number and position, for DSSC with triphenylamine (TPA) as a donor moiety and cyanoacrylic acid (CA) as an acceptor one. And it is found that the best optical response was obtained when only one BTD was introduced on the side of the acceptor moiety.
<Keywords:> Organic dyes, Dye sensitized solar cells, Conjugation order, Optoelectronic properties, Benzothiadiazole
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/3/20_2021-0038/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, 94-96, by J-STAGE]
<Title:> HSP90とコシャペロンp23複合体の安定性に関するシミュレーション研究
<Author(s):> 松倉　里紗, 宮下　尚之
<Corresponding author E-Mill:> miya(at)waka.kindai.ac.jp
<Abstract:> Heat Shock Protein 90 (HSP90) has been known as one of the molecular chaperone proteins, and it supports the correct folding of client proteins. It has been getting attention as the target protein for an anti-cancer drug because the client proteins sometimes include the critical proteins of progressing cancer. In the HSP90 chaperon cycle, several co-chaperones and substrates interact with HSP90 in turn. In this study, we focused on the interaction between HSP90 and p23, which is one of the co-chaperones. After the HSP90 dimer forms the closed conformation, the p23 and ATP bind to the HSP90. However, the detailed interaction among them has not been clear yet. To clear the mechanism of the interaction among HSP90, ATP, and p23, we performed the all-atom molecular dynamics simulations of ATP bound/unbound HSP90 with/without p23. We found that the domain swapping in HSP90 closed conformation is essential for the stable binding between HSP90 and p23, and the ATP binding supports the stability of the HSP90 and p23 complex.
<Keywords:> Molecular Dynamics Simulation, Co-chaperone, Heat Shock Protein 90, Chaperone cycle, Computational Biophysics
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/3/20_2021-0044/_article/-char/ja/