A. Suenaga, Y. Komeiji, M. Uebayasi, T. Meguro, I. Yamato
a Department of Biological Science and Technology, Science University of Tokyo 2641 Yamazaki, Noda-shi, Chiba 278-8510, Japan *e-mail: yamato @yl05hp. tb. noda. sut. ac. jp (tel. +81-471-24-1501 ex.4405; fax. +81-471-25-1841) bSupermolecular Science Division , Electrotechnical Laboratory 1-1-4 Umezono, Tsukuba-shi, Ibaraki 305-0045, Japan c Specific Metabolism Laboratory, National Institute of Bioscience and Human Technology 1-1-3 Higashi, Tsukuba-shi, Ibaraki 305-0046, Japan
{"title":"Molecular dynamics simulation of unfolding of histidine-containing phosphocarrier protein in water.","authors":"A. Suenaga, Y. Komeiji, M. Uebayasi, T. Meguro, I. Yamato","doi":"10.2477/JCHEMSOFT.4.127","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.4.127","url":null,"abstract":"a Department of Biological Science and Technology, Science University of Tokyo 2641 Yamazaki, Noda-shi, Chiba 278-8510, Japan *e-mail: yamato @yl05hp. tb. noda. sut. ac. jp (tel. +81-471-24-1501 ex.4405; fax. +81-471-25-1841) bSupermolecular Science Division , Electrotechnical Laboratory 1-1-4 Umezono, Tsukuba-shi, Ibaraki 305-0045, Japan c Specific Metabolism Laboratory, National Institute of Bioscience and Human Technology 1-1-3 Higashi, Tsukuba-shi, Ibaraki 305-0046, Japan","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"45 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1998-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127930791","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}
Takeshi Uno, Haruhisa Hayashi, K. Yamana, H. Nakano
タンパク質立体構造表示プログラムであるModrast-Pの機能を拡張し、立体構造のデータをVirtual Reality Modeling Language (VRML) のデータ形式に変換する機能を加えた。この機能を使うことによって、Modrast-Pで表示されている分子模型をそのままVRML形式のデータに変換することができる。これにより、これまでいくつかの問題があったコンピュータネットワーク上での分子模型のやりとりがVRMLをもちいることによって簡単かつ迅速に行えるようになると期待される。
扩展蛋白质立体结构显示程序modust - p的功能，将立体结构数据Virtual Reality Modeling Language (VRML)的转换为数据格式的功能。通过使用该功能，可以将modust - p显示的分子模型直接转换成VRML格式的数据。通过VRML，一直以来存在诸多问题的计算机网络分子模型交换将变得简单快捷。
{"title":"A Display of Biopolymer Using Virtual Reality Modeling Language","authors":"Takeshi Uno, Haruhisa Hayashi, K. Yamana, H. Nakano","doi":"10.2477/jchemsoft.4.157","DOIUrl":"https://doi.org/10.2477/jchemsoft.4.157","url":null,"abstract":"タンパク質立体構造表示プログラムであるModrast-Pの機能を拡張し、立体構造のデータをVirtual Reality Modeling Language (VRML) のデータ形式に変換する機能を加えた。この機能を使うことによって、Modrast-Pで表示されている分子模型をそのままVRML形式のデータに変換することができる。これにより、これまでいくつかの問題があったコンピュータネットワーク上での分子模型のやりとりがVRMLをもちいることによって簡単かつ迅速に行えるようになると期待される。","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"30 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1998-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131999770","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}
{"title":"Exhaustive Parallel Conformational Search of Pyrethroids and Structure Similarity Study","authors":"H. Chuman, M. Karasawa, M. Sasaki, U. Nagashima","doi":"10.2477/JCHEMSOFT.4.143","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.4.143","url":null,"abstract":"","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"15 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1998-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122002143","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}
{"title":"Automatic Measuring System for Hydrogen Ion Concentration in Rainfall","authors":"Takashi Tanaka","doi":"10.2477/JCHEMSOFT.4.113","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.4.113","url":null,"abstract":"","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"34 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1998-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133340718","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}
MOLDA for Java, a platform-independent molecular modeling and molecular graphics program written in the Java language, is presented. The molecular coordinates in MOLDA, XMol and Protein Data Bank formats can be transferred to the VRML1.0/2.0 format le and can be viewed as a molecular model by using a VRML viewer on the World Wide Web. This program can also be used as an interface to the semi-empirical molecular orbital program MOPAC and the ab initio molecular orbital program GAUSSIAN 94.
介绍了用Java语言编写的独立于平台的分子建模和分子图形程序MOLDA for Java。MOLDA、XMol和Protein Data Bank格式的分子坐标可以转换为VRML1.0/2.0格式，并可以通过在万维网上使用VRML查看器来查看分子模型。该程序还可以作为半经验分子轨道程序MOPAC和从头算分子轨道程序高斯94的接口。
{"title":"MOLDA for Java-A Platform-independent Molecular Modeling and Molecular Graphics Program Written in the Java Language","authors":"H. Yoshida, H. Matsuura","doi":"10.2477/JCHEMSOFT.4.81","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.4.81","url":null,"abstract":"MOLDA for Java, a platform-independent molecular modeling and molecular graphics program written in the Java language, is presented. The molecular coordinates in MOLDA, XMol and Protein Data Bank formats can be transferred to the VRML1.0/2.0 format le and can be viewed as a molecular model by using a VRML viewer on the World Wide Web. This program can also be used as an interface to the semi-empirical molecular orbital program MOPAC and the ab initio molecular orbital program GAUSSIAN 94.","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"401 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1998-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124323329","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}
Yuji Shinohara, T. Nakajima, Satoshi Suzuki, S. Mishima, H. Ishikawa
A computational chemical investigation has been made into the mechanisms of the dehydration and the dehydrogenation of ethanol on six oxide catalysts (SiO2, TiO2, ZnO, MnO, MgO and CdO) using the DV-Xα method. Transition state models of the consecutive mechanism including ethoxide formation and the concerted mechanism proposed by Eucken and Wicke were computed.By comparing the computed results with experimental ones published in the literature, it was concluded that the consecutive mechanism is more reasonable than the concerted one. It was also concluded that the rate-determing step of the ethanol dehydration is for a β-hydrogen shift to a surface oxide ion and that the ease of theshift is a factor controlling the dehydration/ dehydrogenation selectivities of oxide catalysts.
{"title":"A Computational Chemical Investigation of the Dehydration and Dehydrogenation of Ethanol on Oxide Catalysts","authors":"Yuji Shinohara, T. Nakajima, Satoshi Suzuki, S. Mishima, H. Ishikawa","doi":"10.2477/JCHEMSOFT.4.89","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.4.89","url":null,"abstract":"A computational chemical investigation has been made into the mechanisms of the dehydration and the dehydrogenation of ethanol on six oxide catalysts (SiO2, TiO2, ZnO, MnO, MgO and CdO) using the DV-Xα method. Transition state models of the consecutive mechanism including ethoxide formation and the concerted mechanism proposed by Eucken and Wicke were computed.By comparing the computed results with experimental ones published in the literature, it was concluded that the consecutive mechanism is more reasonable than the concerted one. It was also concluded that the rate-determing step of the ethanol dehydration is for a β-hydrogen shift to a surface oxide ion and that the ease of theshift is a factor controlling the dehydration/ dehydrogenation selectivities of oxide catalysts.","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"27 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1998-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124337771","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}
{"title":"Development of A File Conversion Program for Chemical Structure Data: MOLCONV. Traensplantation of the MOLCONV program from PC-9801 for IBM personal computer.","authors":"K. Hayami","doi":"10.2477/jchemsoft.4.119","DOIUrl":"https://doi.org/10.2477/jchemsoft.4.119","url":null,"abstract":"","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"37 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1998-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132422303","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}
A program to construct a fundamental and original starting material library to embody starting material-oriented retrosynthetic analysis in the AIPHOS system has been developed. The data in the library can be registered automatically from ACD, a commercial chemical structure database, by utilizing this program. This program recognizes synthetic equivalents to categorize functional groups. The resultant library is made up of a hierarchical structure using abstract graphs. The structure, the constructing method of the starting material library for AIPHOS and the registration results of data selected at random from ACD are described. In addition, a brief outline of AIPHOS is included.
{"title":"Development of a Program for Construction of a Starting Material Library for AIPHOS","authors":"K. Satoh, S. Azuma, Hiroko Satoh, K. Funatsu","doi":"10.2477/JCHEMSOFT.4.101","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.4.101","url":null,"abstract":"A program to construct a fundamental and original starting material library to embody starting material-oriented retrosynthetic analysis in the AIPHOS system has been developed. The data in the library can be registered automatically from ACD, a commercial chemical structure database, by utilizing this program. This program recognizes synthetic equivalents to categorize functional groups. The resultant library is made up of a hierarchical structure using abstract graphs. The structure, the constructing method of the starting material library for AIPHOS and the registration results of data selected at random from ACD are described. In addition, a brief outline of AIPHOS is included.","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1998-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129575080","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}
{"title":"Neural Network Reproduction of Time Series Data with Varying Amplitudes and Frequencies","authors":"Mitsue Onodera, U. Nagashima, Hiroaki Yoshida, T. Aoyama, H. Hosoya","doi":"10.2477/JCHEMSOFT.4.57","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.4.57","url":null,"abstract":"生体の断層イメージを測定する核磁気共鳴のシグナルやBelousov-Zhabotinsky反応 (BZ) などの振動反応の酸化還元ポテンシャルは、振幅と周期が時間とともに変化していく時系列データである。しかし、従来の統計的手法では振幅変化及び周期変化を同時に追うことは困難であり、その予測は難しかった。そこで本研究では、時間とともに振幅と周期が同時に変化する時系列データの予測を行うために、ニューラルネットワークからなるモデルを構築した。このモデルは、振幅変化及び周期変化の予測を行うための2つのニューラルネットワークと、それらを統括する一つのニューラルネットワークからなる。本モデルを用いて4種類のモデル関数による数値実験を行い、最小自乗法を用いた際の結果と比較したところ、学習区間においては最小自乗法の方が高い傾向があるが、予測区間においては本モデルの方が精度が高いことがわかった。特に振幅変化の予測では本モデルの方が高い精度を得ることができることがわかった。","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1998-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131703558","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}
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