Journal of Computer Aided Chemistry最新文献_第8页

Structural Features of the Nucleotide Sequences of Genomes 基因组核苷酸序列的结构特征

Journal of Computer Aided Chemistry Pub Date : 2009-01-01 DOI: 10.2751/JCAC.10.38

M. Takeda, M. Nakahara

{"title":"Structural Features of the Nucleotide Sequences of Genomes","authors":"M. Takeda, M. Nakahara","doi":"10.2751/JCAC.10.38","DOIUrl":"https://doi.org/10.2751/JCAC.10.38","url":null,"abstract":"We propose structural features of genomic DNA, which are essential to generate and to analyze genome. We calculated the appearance frequency of the nucleotides (bases) of throughout the entire genome as a polynucleotide molecule consisting of Adenine (A), Thymine (T), Guanine (G) and Cytosine (C) bases including the coding- and the non-coding regions, primarily in the genomes of Saccharomyces cerevisiae, Escherichia coli, and Homo sapiens. Our results indicate that the base sequences in a single-strand of DNA have the following characteristics: (1) reverse-complement symmetry of 3-9 successive bases, (2) bias and (3) multiple fractality of the distribution of four bases, A, T, G and C depending on the distance, exponentially decreased at short distances and linearly decreased at long distances in double logarithmic plot (power spectrum) of L (the distance of a base to the next base) vs P (L) (the probability of the base-distribution at L). These structural features of a single-strand of DNA can be clearly observed in any genomic DNA, especially observed remarkable in eukaryotic genome. Whereas in the artificial genomes or chromosomes with the same base-numbers, the same base-contents and the same frequencies of 64 triplets, the bias and the linearly-decreased fractality of the distribution of four bases described the above were missing, although the reverse-complement symmetry of the base sequences and the exponentially decreased-fractality of the base distribution were observed.","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"10 1","pages":"38-52"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69254629","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: 8

Fragment MO Calculations on Specific Interactions between AhR and TCDD for Beluga and Tern 白鲸和燕鸥AhR和TCDD特异性相互作用的片段MO计算

Journal of Computer Aided Chemistry Pub Date : 2009-01-01 DOI: 10.2751/JCAC.10.63

Satoshi Miyagi, Eri Yoshikawa, Kenichi Dedachi, S. Itoh, M. Ishihara-Sugano, N. Kurita

{"title":"Fragment MO Calculations on Specific Interactions between AhR and TCDD for Beluga and Tern","authors":"Satoshi Miyagi, Eri Yoshikawa, Kenichi Dedachi, S. Itoh, M. Ishihara-Sugano, N. Kurita","doi":"10.2751/JCAC.10.63","DOIUrl":"https://doi.org/10.2751/JCAC.10.63","url":null,"abstract":"芳香族炭化水素受容体(AhR: Arylhydrocarbon receptor)は、内分泌撹乱物質等の外来異物が生体内に取り込まれた時に、これらを結合し、その情報を核に伝え、代謝酵素の発現を誘導することが明らかになっている。しかし、AhRの立体構造及びAhRと外来異物との相互作用機構は未解明である。本研究では、この機構を解明するため、シロイルカ及びアジサシのAhRと、代表的な内分泌撹乱物質であるダイオキシン(TCDD: 2,3,7,8-tetrachrodibenzo-p-dioxin)の複合体構造を作成し、その特異的相互作用を、古典分子力学法及びFragment分子軌道法を用いた分子シミュレーションにより、原子・電子レベルで解析した。その結果、2種類のAhR中の42番目のアミノ酸の相違が、AhRとTCDD間の相互作用に大きな影響を与え、シロイルカのAhRがアジサシのAhRよりも強くTCDDを結合することが明らかになった。この結果は、シロイルカの方がTCDDに対し感受性が高いとする実験結果を定性的に説明出来る。","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"10 1","pages":"63-75"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69254654","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

ステレオへテロトピックな関係ではなくRS-ジアステレオトピックな関係により決定したpro-R/pro-S-記述子立体声由RS-二体而不是恐怖主题关系决定的pro-R/pro-S-描述符

Journal of Computer Aided Chemistry Pub Date : 2009-01-01 DOI: 10.2751/JCAC.10.76

眞作藤田

{"title":"ステレオへテロトピックな関係ではなくRS-ジアステレオトピックな関係により決定したpro-R/pro-S-記述子","authors":"眞作藤田","doi":"10.2751/JCAC.10.76","DOIUrl":"https://doi.org/10.2751/JCAC.10.76","url":null,"abstract":"The pro-R/pro-S system has been redefined by using the concept of pro-RS-stereogenicity, where two ligands in an RS-diastereotopic relationship are pairwise characterized by pro-R- and pro-S-descriptors on the basis of stereoisograms. As for a practical criterion for determining RS-diastereotopic relationships, a symmetry criterion has been developed as a new matter by extending the concept of stereoisograms to testify RS-diastereotopic relationships. The conventional definitions of pro-R/pro-S-descriptors which are based on the original term \"prochirality\" (along with enantiotopic and diastereotopic relationships) and on the revised term \"prostereogenicity\" (along with stereoheterotopic relationships) are altogether abandoned. The revised concept of prochirality has a purely geometric meaning, which stems from the term enantiotopic relationship or equivalently enantiospheric equivalence class (S. Fujita, Symmetry and Combinatorial Enumeration in Chemistry, Springer-Verlag, Berlin-Heidelberg (1991)).The two concepts for describing intramolecular environments, i.e., the pro-RS-stereogenicity and the prochirality, are clarified to correspond to the concepts of RS-stereogenicity and chirality, which have been formulated on the basis of stereoisograms in order to bring about a harmonized viewpoint to stereoisomeric and geometric intermolecular features of stereochemistry (S. Fujita, J. Org. Chem., 69, 3158-3165 (2004); J. Comput. Aided Chem., 10, 16-29 (2009)). Chirality-faithfulness of pro-R/pro-S-descriptors specified by RS-diastereotopic relationships is discussed to harmonize pro-RS-stereogenicity with prochirality.","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"10 1","pages":"76-95"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2751/JCAC.10.76","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69254204","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: 12

Inverse QSAR Study Using Evolutionary Algorithm 基于进化算法的QSAR逆研究

Journal of Computer Aided Chemistry Pub Date : 2009-01-01 DOI: 10.2751/JCAC.10.10

K. Hasegawa, Toshiro Kimura, K. Funatsu

{"title":"Inverse QSAR Study Using Evolutionary Algorithm","authors":"K. Hasegawa, Toshiro Kimura, K. Funatsu","doi":"10.2751/JCAC.10.10","DOIUrl":"https://doi.org/10.2751/JCAC.10.10","url":null,"abstract":"定量的構造―活性相関 (Quantitative Structure-Activity Relationship: QSAR) は、古くから行われており、成功例も多い。しかしながら、予測精度の高いモデルを構築すると、逆にモデルの解釈が難しくなり、設計が困難な場合が多い。そこで、任意の構造をコンピュータで発生させて、モデルの予測値が高い構造だけを自動発生するQSAR逆設計のシステムを構築した。システムのコアとなる構造発生部分については、EA-Inventor (Evolutionary Algorithm-Inventor) を利用した。 SMILEで表記した初期構造を入力すると、交差、変異などの操作で新たな構造を生成する。発生した構造をQSARモデルで予測して、予測値をスコアとして返す。スコアが高い構造は残して、さらに、新たな構造を生成する。このような操作を複数回繰り返して、高いスコアを持つ構造が十分そろったら終了する。EA-Inventorを文献のトリプシン阻害剤データに適用した。スコアに利用するQSARモデルとして、CoMFA (comparative molecular field analysis) を採用した。学習セットと大きく異なる構造が発生した場合には、高いペナルティー値を加え、発生構造が学習セットから大きく逸脱しないように工夫をした。出力された構造は、トリプシンの構造と高い相補性を持っており、高い阻害活性が期待できる。今回は、阻害活性のQSARモデルの応用であるが、これに、ADME (absorption, distribution, metabolism, excretion) モデルや合成の難易度を加えることもできるので、より実用的な薬物設計が可能である。","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"71 1","pages":"10-15"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69254534","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: 4

Signal Detection of Drug Complications Applying Association Rule Learning for Stevens-Johnson Syndrome 基于关联规则学习的Stevens-Johnson综合征药物并发症信号检测

Journal of Computer Aided Chemistry Pub Date : 2009-01-01 DOI: 10.2751/JCAC.10.118

Yuko Shirakuni, Kousuke Okamoto, N. Kawashita, T. Yasunaga, T. Takagi

{"title":"Signal Detection of Drug Complications Applying Association Rule Learning for Stevens-Johnson Syndrome","authors":"Yuko Shirakuni, Kousuke Okamoto, N. Kawashita, T. Yasunaga, T. Takagi","doi":"10.2751/JCAC.10.118","DOIUrl":"https://doi.org/10.2751/JCAC.10.118","url":null,"abstract":"The adverse events induced by drugs have been complicated, when two or more drugs are administrated for a patient. We selected \"Stevens-Johnson Syndrome (SJS) \" as a research object, which is one of the severe skin manifestations. The data source is a database constructed by the Food and Drug Administration (FDA). FDA's post-marketing safety surveillance program is supported by the Adverse Event Reporting System (AERS). AERS is designed with a computerized information database. To analyze the relationships between the concurrent medication and SJS in this study, we applied association rule learning. Our purpose is to propose an efficient procedure that enables the detection of signals for drugs related to an adverse event, without assuming the involvement of a specific drug. We defined new value K for the evaluation of existing signal detection. Association rule was evaluated according to criterion K value. As a result, it was suggested to obtain a strong signal by combining two concomitant drugs. Association rule learning in this study was applicable for the analysis of the relationships between adverse events and pairs of drugs.","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"10 1","pages":"118-127"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2751/JCAC.10.118","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69254552","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: 7

Kernel Partial Least Squaresによる化学物質の生分解性予測 Kernel Partial Least Squares对化学物质可降解性的预测

Journal of Computer Aided Chemistry Pub Date : 2009-01-01 DOI: 10.2751/JCAC.10.1

廣松康一, 高原淳一, 西原力, 岡本晃典, 安永照雄, 大眉佳大, 高木達也, 中園金吾

引用次数: 3

RS-ステレオジェニシティーによるRS-立体記述子の決定およびそれらのキラリティー忠実性 RS-立体声定义RS-立体描述符及其闪闪发光保真性

Journal of Computer Aided Chemistry Pub Date : 2009-01-01 DOI: 10.2751/JCAC.10.16

眞作藤田

引用次数: 27

Design of Alkanol Amine Structure for CO2 Absorption Method 二氧化碳吸收法中烷醇胺结构的设计

Journal of Computer Aided Chemistry Pub Date : 2009-01-01 DOI: 10.2751/JCAC.10.96

Naoya Yamashiro, Tomoyuki Miyao, Masamoto Arakawa, K. Funatsu

{"title":"Design of Alkanol Amine Structure for CO2 Absorption Method","authors":"Naoya Yamashiro, Tomoyuki Miyao, Masamoto Arakawa, K. Funatsu","doi":"10.2751/JCAC.10.96","DOIUrl":"https://doi.org/10.2751/JCAC.10.96","url":null,"abstract":"大気中の二酸化炭素濃度の上昇を抑制するための手法として、二酸化炭素地中貯留技術が注目されている。しかし、その実用化のためにはコストの高さが大きな課題となっており、特に二酸化炭素を分離回収する過程におけるコストが全体の大部分を占めると試算されている。そこで本研究ではアルカノールアミン溶液を用いた化学吸収法による二酸化炭素の分離回収に着目し、より優れたアルカノールアミンの設計を目指した。アルカノールアミン溶液は低温下で二酸化炭素を吸収し、加熱により吸収した二酸化炭素を放散する性質があり、二酸化炭素の分離回収に利用することが可能である。吸収液に求められる性質として、二酸化炭素を放散させるために必要な熱量が少なく、吸収速度が速いことが挙げられる。そこで、これらの要求を満たすような吸収液の開発を目的とした。まず、反応熱、吸収速度の実験データを基に、アミンの構造情報からこれらを予測する回帰モデルをPLS (partial least squares)法、GAPLS (genetic algorithm based-PLS)法を用いて構築した。その結果、GAPLS法では反応熱に対してR2=0.999、Q2=0.990、吸収速度に対してR2=0.957、Q2=0.914となり、予測精度の高いモデルが構築された。このモデルを用いて、コンピュータ内で仮想的に発生させた新規構造の物性値を予測することで、有望な物性を持つと予想される吸収液の探索を行った。その結果、実験データよりも良好な物性を示すと考えられる候補構造が複数得られた。","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"10 1","pages":"96-103"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69254215","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

Development of Predictive Models and Reverse Analysis Method for Polymer Design 聚合物设计预测模型与逆向分析方法的发展

Journal of Computer Aided Chemistry Pub Date : 2009-01-01 DOI: 10.2751/JCAC.10.30

S. Goto, Masamoto Arakawa, K. Funatsu

{"title":"Development of Predictive Models and Reverse Analysis Method for Polymer Design","authors":"S. Goto, Masamoto Arakawa, K. Funatsu","doi":"10.2751/JCAC.10.30","DOIUrl":"https://doi.org/10.2751/JCAC.10.30","url":null,"abstract":"現在、ポリマーは多種多様な製品の材料として幅広い用途で利用されている。ポリマーの開発においては、それぞれの用途に応じた設計を行うことが必要であるが、用途によって要求される物性は異なるため、効率的なポリマー設計の手法が求められている。そこで本研究では、物性推算モデルの構築とその逆解析により、要求される物性を実現するポリマーを設計するための方法を提案した。単重合ポリマーデータに対して、原子団寄与法とRDF記述子を用いて予測的な物性推算モデルを構築した。また、ランダム共重合ポリエステルデータに対して、組成や原子団寄与法による物性推算モデルを構築し、モデルの逆解析を通じて複数物性の同時最適化を行った。さらに、既存モノマーの組成検討だけではなく、新規モノマーの構造生成によるポリマー設計手法の提案を行った。いずれの解析においても良好な結果が得られ、情報化学的手法によるポリマー設計の可能性が示された。","PeriodicalId":41457,"journal":{"name":"Journal of Computer Aided Chemistry","volume":"10 1","pages":"30-37"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2751/JCAC.10.30","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69254621","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

Prediction Models for Soil Properties Using VIS-NIR Spectroscopy 基于VIS-NIR光谱的土壤性质预测模型

Journal of Computer Aided Chemistry Pub Date : 2009-01-01 DOI: 10.2751/JCAC.10.53

Masaya Ando, Masamoto Arakawa, K. Funatsu

引用次数: 8