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Application of Model Core Potentials to Zn- and Mg-containing Metalloproteins in the Fragment Molecular Orbital Method 模型核电位在含锌和含镁金属蛋白片段分子轨道法中的应用
IF 0.3
Chem-Bio Informatics Journal Pub Date : 2023-07-20 DOI: 10.1273/cbij.23.14
Koichiro Kato, Ami Yamamoto, C. Watanabe, Kaori Fukuzawa
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引用次数: 0
How Beneficial or Threatening is Artificial Intelligence? 人工智能是有益的还是有威胁的?
IF 0.3
Chem-Bio Informatics Journal Pub Date : 2023-02-20 DOI: 10.1273/cbij.23.7
T. Takagi
{"title":"How Beneficial or Threatening is Artificial Intelligence?","authors":"T. Takagi","doi":"10.1273/cbij.23.7","DOIUrl":"https://doi.org/10.1273/cbij.23.7","url":null,"abstract":"","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":"21 1","pages":""},"PeriodicalIF":0.3,"publicationDate":"2023-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84524533","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
Difficulties and prospects of data curation for ADME in silico modeling 计算机建模中ADME数据管理的困难与展望
IF 0.3
Chem-Bio Informatics Journal Pub Date : 2023-01-13 DOI: 10.1273/cbij.23.1
Tsuyoshi Esaki, Kazuyoshi Ikeda
{"title":"Difficulties and prospects of data curation for ADME in silico modeling","authors":"Tsuyoshi Esaki, Kazuyoshi Ikeda","doi":"10.1273/cbij.23.1","DOIUrl":"https://doi.org/10.1273/cbij.23.1","url":null,"abstract":"","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":"98 1","pages":""},"PeriodicalIF":0.3,"publicationDate":"2023-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76031728","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
Multiple Logistic Regression Modeling of Compound Class as Active or Inactive Against COX-2 and Prediction on Designed Coxib Derivatives and Similar Compounds 抗COX-2活性或非活性化合物类别的多元Logistic回归模型及设计的Coxib衍生物和类似化合物的预测
IF 0.3
Chem-Bio Informatics Journal Pub Date : 2022-10-31 DOI: 10.1273/cbij.22.63
Liza T. Billones*, Alex C. Gonzaga
{"title":"Multiple Logistic Regression Modeling of Compound Class as Active or Inactive Against COX-2 and Prediction on Designed Coxib Derivatives and Similar Compounds","authors":"Liza T. Billones*, Alex C. Gonzaga","doi":"10.1273/cbij.22.63","DOIUrl":"https://doi.org/10.1273/cbij.22.63","url":null,"abstract":"","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":"13 1","pages":""},"PeriodicalIF":0.3,"publicationDate":"2022-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87676533","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: 2
Fragment molecular orbital calculations containing Mg2+ ions: PPlase domain of Cyclophilin G 含Mg2+离子的片段分子轨道计算:亲环蛋白G的PPlase结构域
IF 0.3
Chem-Bio Informatics Journal Pub Date : 2022-09-16 DOI: 10.1273/cbij.22.55
Masayasu Fujii, C. Watanabe, Kaori Fukuzawa, S. Tanaka
{"title":"Fragment molecular orbital calculations containing Mg2+ ions: PPlase domain of Cyclophilin G","authors":"Masayasu Fujii, C. Watanabe, Kaori Fukuzawa, S. Tanaka","doi":"10.1273/cbij.22.55","DOIUrl":"https://doi.org/10.1273/cbij.22.55","url":null,"abstract":"","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":"13 1","pages":""},"PeriodicalIF":0.3,"publicationDate":"2022-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76597932","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
Prediction Models for Fraction of Absorption and Membrane Permeability using Mordred Descriptors 利用莫德雷德描述符的吸收分数和膜透性预测模型
IF 0.3
Chem-Bio Informatics Journal Pub Date : 2022-09-09 DOI: 10.1273/cbij.22.46
Tsuyoshi Esaki, Tomoki Yonezawa, Daisuke Yamazaki, Kazuyoshi Ikeda
{"title":"Prediction Models for Fraction of Absorption and Membrane Permeability using Mordred Descriptors","authors":"Tsuyoshi Esaki, Tomoki Yonezawa, Daisuke Yamazaki, Kazuyoshi Ikeda","doi":"10.1273/cbij.22.46","DOIUrl":"https://doi.org/10.1273/cbij.22.46","url":null,"abstract":"","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":"36 1","pages":""},"PeriodicalIF":0.3,"publicationDate":"2022-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81290117","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
Benchmark of 3D conformer generation and molecular property calculation for medium-sized molecules 中型分子三维构象生成及分子性质计算基准
IF 0.3
Chem-Bio Informatics Journal Pub Date : 2022-09-02 DOI: 10.1273/cbij.22.38
Tomoki Yonezawa, Tsuyoshi Esaki, Kazuyoshi Ikeda
{"title":"Benchmark of 3D conformer generation and molecular property calculation for medium-sized molecules","authors":"Tomoki Yonezawa, Tsuyoshi Esaki, Kazuyoshi Ikeda","doi":"10.1273/cbij.22.38","DOIUrl":"https://doi.org/10.1273/cbij.22.38","url":null,"abstract":"","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":"1 1","pages":""},"PeriodicalIF":0.3,"publicationDate":"2022-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89554396","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
Biological Significance of Intrinsically Disordered Protein Structure 内在无序蛋白质结构的生物学意义
IF 0.3
Chem-Bio Informatics Journal Pub Date : 2022-05-31 DOI: 10.1273/cbij.22.26
M. Sato
{"title":"Biological Significance of Intrinsically Disordered Protein Structure","authors":"M. Sato","doi":"10.1273/cbij.22.26","DOIUrl":"https://doi.org/10.1273/cbij.22.26","url":null,"abstract":"","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":"46 1","pages":""},"PeriodicalIF":0.3,"publicationDate":"2022-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81287823","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
FMO calculations for zinc metalloprotease:Fragmentation of amino-acid residues coordinated to zinc ion 锌金属蛋白酶的FMO计算:与锌离子协调的氨基酸残基的碎片化
IF 0.3
Chem-Bio Informatics Journal Pub Date : 2022-05-12 DOI: 10.1273/cbij.22.21
Kyohei Imai, Daichi Takimoto, Ryosuke Saito, C. Watanabe, Kaori Fukuzawa, Kurita Noriyuki
{"title":"FMO calculations for zinc metalloprotease:Fragmentation of amino-acid residues coordinated to zinc ion","authors":"Kyohei Imai, Daichi Takimoto, Ryosuke Saito, C. Watanabe, Kaori Fukuzawa, Kurita Noriyuki","doi":"10.1273/cbij.22.21","DOIUrl":"https://doi.org/10.1273/cbij.22.21","url":null,"abstract":"We investigated electronic states of a complex of zinc metalloprotease ubiquitin ligase 2 (UBR2) with its peptide ligand using ab initio fragment molecular orbital (FMO) calculations. UBR2 possesses three Zn ions and several residues of UBR2 are coordinated to each Zn ion to form an active site of UBR2. To provide a precise description of these coordination bonds, we included these residues in the same fragment as Zn ion in FMO calculations. The results revealed that all coordinated residues should be included in the same fragment as Zn ion for obtaining the converged results. This fact can be applicable equally to metalloproteases including other metal ions.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":"79 1","pages":""},"PeriodicalIF":0.3,"publicationDate":"2022-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82302183","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
Estimation of the Diffusion Coefficients of Small Molecules by Diffusion Measurements with Agar-gel and Theoretical Molecular Modeling 用琼脂凝胶扩散测量和理论分子模型估计小分子的扩散系数
IF 0.3
Chem-Bio Informatics Journal Pub Date : 2022-04-30 DOI: 10.1273/cbij.22.13
S. Miyamoto, K. Shimono
{"title":"Estimation of the Diffusion Coefficients of Small Molecules by Diffusion Measurements with Agar-gel and Theoretical Molecular Modeling","authors":"S. Miyamoto, K. Shimono","doi":"10.1273/cbij.22.13","DOIUrl":"https://doi.org/10.1273/cbij.22.13","url":null,"abstract":"","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":"6 1","pages":""},"PeriodicalIF":0.3,"publicationDate":"2022-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75249063","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
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