Koichiro Kato, Ami Yamamoto, C. Watanabe, Kaori Fukuzawa
{"title":"Application of Model Core Potentials to Zn- and Mg-containing Metalloproteins in the Fragment Molecular Orbital Method","authors":"Koichiro Kato, Ami Yamamoto, C. Watanabe, Kaori Fukuzawa","doi":"10.1273/cbij.23.14","DOIUrl":"https://doi.org/10.1273/cbij.23.14","url":null,"abstract":"","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":"31 1","pages":""},"PeriodicalIF":0.3,"publicationDate":"2023-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79820322","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":"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}
{"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}
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.
{"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}
{"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}
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