Journal of Computer Aided Chemistry最新文献_第7页

Design Optimization of Photoelectrode Reactor for Hydrogen Production by Combining CFD Simulation and Statistical Methods 基于CFD模拟与统计相结合的光电极制氢反应器设计优化

Journal of Computer Aided Chemistry Pub Date : 2011-01-01 DOI: 10.2751/JCAC.12.1

Y. Maeda, K. Funatsu

引用次数: 0

Advanced PLS Technique Focusing on Visualization and Chemical Interpretation - SOMPLS Analysis of Serine Protease Inhibitors - 聚焦于可视化和化学解释的先进PLS技术-丝氨酸蛋白酶抑制剂的SOMPLS分析

Journal of Computer Aided Chemistry Pub Date : 2010-01-01 DOI: 10.2751/JCAC.11.56

K. Hasegawa, K. Funatsu

{"title":"Advanced PLS Technique Focusing on Visualization and Chemical Interpretation - SOMPLS Analysis of Serine Protease Inhibitors -","authors":"K. Hasegawa, K. Funatsu","doi":"10.2751/JCAC.11.56","DOIUrl":"https://doi.org/10.2751/JCAC.11.56","url":null,"abstract":"In quantitative structure activity relationships (QSAR), partial least squares (PLS) are of particular interest as a statistical method. Since successful applications of PLS to QSAR data set, PLS has evolved for coping with more demands associated with complex data structures. Especially, PLS variants focusing on visualization and chemical interpretation are highly desirable for molecular design. In this paper, we employed the self-organized map PLS (SOMPLS) approach to predict multiple inhibitory activities against three serine protease receptors (Factor Xa, Tryptase and urokinase-type Plasminogen Activator (uPA)). Retrosynthetic Combinatorial Analysis Procedure (RECAP) fingerprints were used as chemical descriptors that express the existence of specific substructure in the molecule. From the SOMPLS analysis and the subsequent correlation map, essential fragments for each serine protease were easily identified. From the correlation map, we designed best combinations of fragments at each substituent position for each serine protease protein. The essential fragments could be validated from X-ray crystal structures of serine protease receptors in computer graphics. SOMPLS is an unique approach that makes data-mining feasible from visualization of structure-activity data biased to ligand-based view point.","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"11 1","pages":"56-61"},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69254742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Ab initio MO Study of Hydrogen Bonding and Spectral Characteristics of HCN-H2O-HCN Trimer: Comparison between Dimer and Trimer HCN-H2O-HCN三聚体氢键和光谱特性的从头计算研究:二聚体和三聚体的比较

Journal of Computer Aided Chemistry Pub Date : 2010-01-01 DOI: 10.2751/jcac.11.36

Tomoya Takada, Shugo Ohshita

引用次数: 0

Forest Learning Method for Chemical Education 化学教育的森林学习法

Journal of Computer Aided Chemistry Pub Date : 2010-01-01 DOI: 10.2751/JCAC.11.1

M. Kaihara

{"title":"Forest Learning Method for Chemical Education","authors":"M. Kaihara","doi":"10.2751/JCAC.11.1","DOIUrl":"https://doi.org/10.2751/JCAC.11.1","url":null,"abstract":"化学は、理解する内容、記憶する内容、また計算力を必要とする内容などを含み、さらに、その原理原則も、電気分解や熱化学方程式、有機化学等、多種多様であることから、学生にとっては、比較的、取組みにくい科目と考えられている。筆者は、従来から、決定木、二進木等、樹木の構造を持つ回帰と分類の方法に関心を持ち、分類条件の探索や判別に応用している。この二進木は、集団学習法の一つ、RandomForestsやboostingの一種、MART(Multiple Additive Regression Trees)等に進化し、高い精度を持つ分類と回帰の方法へと発展した。特に、MARTの、学習率を低くするほど、短時間で高い精度が得られるという特徴、「遅いが早い」という逆説を、化学の教育に活用できないだろうかと考えた。具体的には、オープンエンド型の発想法、マインドマップと、問題解決を見据えた収束型の発想法、思考展開図を併用し、細かな問いかけ（ステップ）の積み重ねによって全体像を把握しようとすることによって、化学の理解深化や知識の定着と授業のコンパクト化を目指す試みである。マインドマップは、樹木の幹と枝葉のような構造を持ち、また、MARTは、簡素な幼木が一列に整列した林に例えられることから、森（マインドマップの集合）と林の概念を基盤とした学習教材とその方法として「森（森林）」と呼称した。H21 年度、SPP(サイエンスパートナーシッププログラム)にて、体験学習講座を開催した結果についても、併せて報告する。","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"11 1","pages":"1-10"},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69254258","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

A Theoretical Study on the Temperature Control of Fabrication of Pentacene Thin Film Transistors from Soluble Pentacene Precursors 可溶并五苯前驱体制备并五苯薄膜晶体管温度控制的理论研究

Journal of Computer Aided Chemistry Pub Date : 2010-01-01 DOI: 10.2751/JCAC.11.62

Kazuaki Yoshimura, R. Ishikawa, H. Miyazaki, Atsushi Kawata, Michinori Sumimoto, K. Hori

{"title":"A Theoretical Study on the Temperature Control of Fabrication of Pentacene Thin Film Transistors from Soluble Pentacene Precursors","authors":"Kazuaki Yoshimura, R. Ishikawa, H. Miyazaki, Atsushi Kawata, Michinori Sumimoto, K. Hori","doi":"10.2751/JCAC.11.62","DOIUrl":"https://doi.org/10.2751/JCAC.11.62","url":null,"abstract":"ペンタセンを用いた塗布型有機半導体素子の作成法として、可溶性のペンタセン前駆体を塗布し逆Diels-Alder反応によりペンタセン骨格から脱離基を脱離させペンタセン薄膜へ転換する方法が提案されている。脱離基を変えた多くの前駆体に対して実験が行われ、それぞれペンタセンへの転換温度が異なることが示された。この転換温度と脱離基構造の関係を明らかにするため、報告されている６つの前駆体からペンタセンが生成する反応の解析を行った。その結果、活性化エネルギーEaが低い前駆体ほど転換温度が低い傾向にあることが明らかとなった。また重回帰解析を用いた検討により脱離基の最低非占有軌道（LUMO）と反応熱ΔEが低いほどEaが低いと計算された。次に、塗布成膜時に残存した溶媒の影響を調べるため、水素結合が形成される位置にメタノール分子を配置して、反応解析を行ったところ、Eaが気相中と比べわずかではあるが（最大で0.7 kcal mol-1）低下することが判明した。これは、前駆体の脱離基設計に加え展開溶媒として用いた分子の寄与を考慮することで、より転換温度の低い成膜プロセスが提案できる可能性を示している。","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"11 1","pages":"62-69"},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2751/JCAC.11.62","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69254787","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Bayesian Classification of Cytochrome P450 3A4 Substrates/Non-substrates and Color Mapping for Chemical Interpretation 细胞色素P450 3A4底物/非底物的贝叶斯分类和化学解释的颜色映射

Journal of Computer Aided Chemistry Pub Date : 2010-01-01 DOI: 10.2751/jcac.11.19

Kiyoshi Hasegawaa, Kimito Funatsub

{"title":"Bayesian Classification of Cytochrome P450 3A4 Substrates/Non-substrates and Color Mapping for Chemical Interpretation","authors":"Kiyoshi Hasegawaa, Kimito Funatsub","doi":"10.2751/jcac.11.19","DOIUrl":"https://doi.org/10.2751/jcac.11.19","url":null,"abstract":"Prediction of cytochrome P450 (CYP) 3A4 substrates is valuable for finding promising drug candidates and a considerable amount of attention has been devoted to in silico predictions. Machine learning (ML) methods have recently been explored for perfoming ligand-based approaches. ML methods utilize supervised learning methods such as neural networks, support vector machines and Bayesian approaches to develop statistical models. In this paper, we used Bayesian approach to classify CYP 3A4 substrates and non-substrates. The extended connectivity fingerprint (ECFP) descriptor was used as chemical descriptor. The atom score was calculated from the Bayesian score of each fingerprint. By visualizing the atom scores with five graded-colors, the color mapping for each compound was performed. This can be used for chemical interpretaion why the specific compound exhibits CYP 3A4 substrate. The established Bayesian model and the associated color mapping would be useful for avoiding the risk of CYP 3A4 substrate in early drug discovery. The parallel use of the prediction of oxidation sites in the subsequent paper can give us de novo prediction of any molecules concerning CYP 3A4.","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2751/jcac.11.19","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69254332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Development of a Pharmacophore Modeling Method and its Application to Phosphodiesterase-4 Inhibitors 磷酸二酯酶-4抑制剂药效团建模方法的建立及其应用

Journal of Computer Aided Chemistry Pub Date : 2010-01-01 DOI: 10.2751/JCAC.11.44

Masamoto Arakawa, M. Shoda, K. Funatsu

{"title":"Development of a Pharmacophore Modeling Method and its Application to Phosphodiesterase-4 Inhibitors","authors":"Masamoto Arakawa, M. Shoda, K. Funatsu","doi":"10.2751/JCAC.11.44","DOIUrl":"https://doi.org/10.2751/JCAC.11.44","url":null,"abstract":"新規医薬品の開発には多くの費用と時間を要するため、その効率化が強く望まれており、そのための有力な方法のひとつが、コンピュータと情報化学を利用して医薬品開発を行うインシリコ創薬である。特に、創薬プロセスの初期段階であるリード探索は、創薬プロセス全体の効率に大きな影響を与えるため、バーチャルスクリーニングによって質の高いリード化合物候補を発見する試みが数多く行われている。バーチャルスクリーニングを行うためのひとつの方法は、既知のリガンドからファーマコフォアモデルを構築し、それをもとにバーチャルライブラリの探索を行うことである。タンパクの立体構造を必要とせず、リガンドのみの情報で解析が可能であるという利点を持っている。ファーマコフォアモデルに基づくバーチャルスクリーニングにおいては、いかにして妥当なファーマコフォアを設定するかが重要であり、これまで様々な手法が提案されているが、決定的な手法は確立されていないのが現状である。そこで我々は、Hopfieldニューラルネットワークを利用して分子構造の重ね合わせを行うことによってファーマコフォアモデルを構築する手法を提案した。そして、その有用性を検証するため、Phosphodiesterase-4（PDE4）の阻害剤についてファーマコフォアモデルの構築を行った。活性を持つことがすでに知られている6つの阻害剤について配座探索を行い、得られた複数の配座のすべての組み合わせについて構造の重ね合わせを行った。そして、その重なりの度合いを指標として活性配座の推定を行い、ファーマコフォアを決定した。得られたファーマコフォアについて、PDE4のX線結晶構造を用いた検証を行った結果、活性部位の構造特徴を的確にとらえた妥当なモデルであることが確認された。","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"11 1","pages":"44-55"},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69254735","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Excitation Energies of Stacked DNA Base Pair 堆叠DNA碱基对的激发能

Journal of Computer Aided Chemistry Pub Date : 2010-01-01 DOI: 10.2751/JCAC.11.25

Muneaki Kamiya

引用次数: 1

Ecotoxicity Prediction Using 3D Descriptors 利用3D描述符进行生态毒性预测

Journal of Computer Aided Chemistry Pub Date : 2010-01-01 DOI: 10.2751/JCAC.11.11

日高伸之介, 白石寛明, 大眉佳大, 山崎広之, 岡本晃典, 川下理日人, 安永照雄, 高木達也

{"title":"Ecotoxicity Prediction Using 3D Descriptors","authors":"日高伸之介, 白石寛明, 大眉佳大, 山崎広之, 岡本晃典, 川下理日人, 安永照雄, 高木達也","doi":"10.2751/JCAC.11.11","DOIUrl":"https://doi.org/10.2751/JCAC.11.11","url":null,"abstract":"A vast quantity of chemicals are present in our environment and are considered indispensable to our high technological society. However, there are some chemicals that are hazardous and that can extensively impact both human health and the global environment. In Japan, ecotoxicity tests of chemical substances have been conducted with the goal of contributing to the Organization for Economic Cooperation and Development (OECD) evaluation program for harmful high-production volume (HPV) chemicals since 1995. To date, only about 500 compounds have been tested. There is a possibility that quantitative structure-activity relationships (QSARs) may enable us to predict environmental toxicities and fates as well as the physical and chemical properties of compounds; therefore, the toxicity prediction by QSARs is a possible alternative to the measurements of their ecotoxicities. In this study, we generated QSAR models from toxicity tests of Daphnids using only 3D descriptors to examine the availability of particular 3D descriptors for predicting of the ecotoxicity of compounds with various structures. Predicton accuracy of the model generated in this study was adequate and improved compared to that of the model using only the n-octanol/water partition coefficient, logP(o/w).","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"40 1","pages":"11-18"},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2751/JCAC.11.11","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69254266","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Selective Search Focusing on Retro-Synthetically Important Bonds in A Synthesis Design System 在一个合成设计系统中聚焦于逆向合成重要键的选择性搜索

Journal of Computer Aided Chemistry Pub Date : 2009-01-01 DOI: 10.2751/JCAC.10.104

A. Tanaka, T. Kawai, T. Takabatake, Hideho Okamoto, M. Bersohn

引用次数: 1