Chem-Bio Informatics Journal最新文献_第9页

Identification of the Dual Action Antihypertensive Drugs Using TFS-Based Support Vector Machines 基于tfs的支持向量机识别双作用降压药

IF 0.3

Chem-Bio Informatics Journal Pub Date : 2009-01-01 DOI: 10.1273/CBIJ.10.E_1

Kentaro Kawai, Yoshimasa Takahashi

引用次数: 16

Molecular geometry-dependent atomic charge calculation with modified charge equilibration method 基于改进电荷平衡法的分子几何相关原子电荷计算

IF 0.3

Chem-Bio Informatics Journal Pub Date : 2009-01-01 DOI: 10.1273/CBIJ.9.30

K. Aoki, S. Tanaka, T. Nakano

引用次数: 4

Validation of ArgusLab Efficiencies for Binding Free Energy Calculations ArgusLab结合自由能计算效率的验证

IF 0.3

Chem-Bio Informatics Journal Pub Date : 2009-01-01 DOI: 10.1273/CBIJ.9.52

A. Oda, O. Takahashi

引用次数: 23

Prediction of fragile points of coiled coils 卷材易碎点预测

IF 0.3

Chem-Bio Informatics Journal Pub Date : 2009-01-01 DOI: 10.1273/CBIJ.9.12

Hideki Tanizawa, M. Taniguchi, Ganga D. Ghimire, S. Mitaku

{"title":"Prediction of fragile points of coiled coils","authors":"Hideki Tanizawa, M. Taniguchi, Ganga D. Ghimire, S. Mitaku","doi":"10.1273/CBIJ.9.12","DOIUrl":"https://doi.org/10.1273/CBIJ.9.12","url":null,"abstract":"A prediction system for identifying the region of flexible regions of the coiled coil was developed to determine the bending positions of the myosin rods using atomic force microscopy (AFM) and to analyze the molecular structures of proteins containing coiled coils. The prediction system comprises two modules: identification of heptad break points and prediction of fragile points in the coiled coil due to the hydrophilic core or hydrophobic outfield region. Here, we investigated the myosin rods using this prediction system. The results of AFM imaging showed four main flexible regions in a single myosin rod and of the 17 possible fragile points predicted, 16 were located in the four experimental bending regions. Next, we examined the enhanced fluctuation around these predicted fragile points using the B-factor for the three dimensional structure of coiled coil proteins from the SCOP database and found that the fluctuations in the hydrophilic core regions were significantly larger than those in the regions of the normal coiled coil. In contrast, the fluctuations in the hydrophobic outfield regions were reduced, suggesting a structural change of the coiled coils to balance these regions. Thus, the dynamic changes in the structure of the coiled coils around the fragile points may be related to the biological functions of the proteins. The prediction tool which developed in this work was incorporated in the SOSUIcoil system which predicts the coiled coil regions.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":"105 1","pages":"12-29"},"PeriodicalIF":0.3,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74476388","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

Pharmacokinetic strategy for designing orally effective prodrugs overcoming biological membrane barriers: proposal of kinetic classification and criteria for membrane-permeable prodrug-likeness 设计克服生物膜屏障的口服有效前药的药代动力学策略:提出动力学分类和膜渗透性前药相似标准

IF 0.3

Chem-Bio Informatics Journal Pub Date : 2008-01-01 DOI: 10.1273/CBIJ.8.25

T. Mizuma

{"title":"Pharmacokinetic strategy for designing orally effective prodrugs overcoming biological membrane barriers: proposal of kinetic classification and criteria for membrane-permeable prodrug-likeness","authors":"T. Mizuma","doi":"10.1273/CBIJ.8.25","DOIUrl":"https://doi.org/10.1273/CBIJ.8.25","url":null,"abstract":"Chemical modification of an active drug with promoiety to a prodrug (“prodrugging”) is a way to improve the pharmacokinetic characteristics of an active drug in the body; however, no kinetic principles have been proposed to design orally effective prodrugs to overcome biological membrane barriers. Therefore, based on a previously reported kinetic model of drug absorption [Mizuma et al., J Pharm. Sci. 85, 854 (1996)], conditional equations for the kinetic strategy of prodrugging were derived. Conditional equations contain terms of uptake (influx) and efflux transport of the prodrug and drug, and the metabolism of the prodrug to drug. Thereby, kinetic classification and criteria for effective membrane-permeable prodrugs are shown as a decision tree with conditional equations. The first point in the kinetic classification and criteria is the uptake process; second, the efflux process is vetted; finally, the metabolic process is elucidated. In some cases, metabolism is not a factor in the better absorption of prodrugs than active drugs. Experiments corresponding to particular processes were proposed, and are applicable to the design of prodrugs not only for intestinal absorption, but also for biological membrane permeation.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":"125 1","pages":"25-32"},"PeriodicalIF":0.3,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89135154","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: 3

Classification and characterization of human full-length cDNA clones that are difficult to sequence 难以测序的人全长cDNA克隆的分类和鉴定

IF 0.3

Chem-Bio Informatics Journal Pub Date : 2008-01-01 DOI: 10.1273/CBIJ.8.1

Akihiko Kishimoto, Yukio Ono, K. Murakawa, T. Ishibashi, A. Wakamatsu, K. Kanehori, N. Nomura, T. Isogai, M. Yohda, S. Sugano

{"title":"Classification and characterization of human full-length cDNA clones that are difficult to sequence","authors":"Akihiko Kishimoto, Yukio Ono, K. Murakawa, T. Ishibashi, A. Wakamatsu, K. Kanehori, N. Nomura, T. Isogai, M. Yohda, S. Sugano","doi":"10.1273/CBIJ.8.1","DOIUrl":"https://doi.org/10.1273/CBIJ.8.1","url":null,"abstract":"In the Full-length Human cDNA Sequencing Project, 30,160 cDNA were sequenced. Among them, our group performed sequencing of 3,588 cDNAs, mainly using the primer walking method. The sequences achieved an average Phrap score of 76, which means the average of expected sequence accuracy was 99.9999975%, by sequencing of both strands with the criterion of a Phrap score over 30. In spite of the extremely high sequence reliability, we met with difficulty in sequencing 52 cDNAs, which are termed undecipherable cDNAs. cDNAs of long repeats were considered as a possible source of sequencing difficulty; their maximum repeat length sequenced by the primer walking method was 530 bp, without using the random method, and 81% of long repeat sequences remained in the ORFs. In single repeat regions, the insertion/deletion rates were much larger than in the usual regions. The fraction of SINE/Alu repeats in the cDNAs was 5.4%, half of the fraction of the human genome. The fraction of SINE/Alu in undecipherable cDNAs was up to 10%, the same level of the human genome.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":"23 1","pages":"1-13"},"PeriodicalIF":0.3,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85575991","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

A high performance prediction system of coiled coil domains containing heptad breaks: SOSUIcoil 一种高性能的含七断点的线圈结构域预测系统:SOSUIcoil

IF 0.3

Chem-Bio Informatics Journal Pub Date : 2008-01-01 DOI: 10.1273/CBIJ.8.96

Hideki Tanizawa, Ganga D. Ghimire, S. Mitaku

{"title":"A high performance prediction system of coiled coil domains containing heptad breaks: SOSUIcoil","authors":"Hideki Tanizawa, Ganga D. Ghimire, S. Mitaku","doi":"10.1273/CBIJ.8.96","DOIUrl":"https://doi.org/10.1273/CBIJ.8.96","url":null,"abstract":"The coiled coil structure in proteins is characterized by heptad repeats of hydrophobic amino acids, but many breaks of the heptad repeats are observed within coiled coil regions which are the main cause of the errors in the currently used prediction systems for coiled coils. For understanding the characteristics of coiled coils including heptad breaks, the features of coiled coils were studies focusing on three problems: (1) the determination of appropriate register for the breaks in heptad repeat regions, (2) the discriminations of coiled coil regions using physical properties of amino acid segments which have heptad repeats and (3) the elucidation of the structural difference among several types of heptad breaks. Appropriate registers of heptad repeats and breaks were determined by two steps: first, the typical template of heptad repeats was applied to amino acid sequences and then several types of template for heptad breaks were applied to the segments around inconsistent points of the heptad repeat regions, leading to the most appropriate registers. Then, the coiled coil regions were discriminated from other types of regions by the canonical discriminant analysis, using ten parameters (three physicochemical properties and seven number densities of amino acids). The novel coiled coil prediction system SOSUIcoil showed better performances of coiled coil prediction than other prediction systems. Furthermore, the structures of segments around the heptad breaks were analyzed, indicating that some types of heptad breaks tend to form coiled coil structure whereas the other types are at the end of coiled coils.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":"21 1","pages":"96-111"},"PeriodicalIF":0.3,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80866636","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

Physicochemical properties of GPCR amino acid sequences for understanding GPCR-G-protein coupling GPCR氨基酸序列的理化性质为了解GPCR- g -蛋白偶联提供依据

IF 0.3

Chem-Bio Informatics Journal Pub Date : 2008-01-01 DOI: 10.1273/CBIJ.8.49

Ganga D. Ghimire, Hideki Tanizawa, M. Sonoyama, S. Mitaku

引用次数: 1

Solvent Site-Dipole Field Accompanying Protein-Ligand Approach Process 溶剂位偶极子场伴随蛋白质配体接近过程

IF 0.3

Chem-Bio Informatics Journal Pub Date : 2008-01-01 DOI: 10.1273/CBIJ.8.14

N. Takano, K. Umezawa, Jinzen Ikebe, Yuki Sonobe, Ryosuke Yagisawa, Ito Junichi, N. Hamasaki, D. Mitomo, H. Miyagawa, A. Yamagishi, J. Higo

引用次数: 7

Application of Rough Set Theory to High Throughput Screening Data for Rational Selection of Lead Compounds 粗集理论在高通量筛选数据中合理选择先导化合物的应用

IF 0.3

Chem-Bio Informatics Journal Pub Date : 2008-01-01 DOI: 10.1273/CBIJ.8.85

Michio Koyama, K. Hasegawa, Masamoto Arakawa, K. Funatsu

{"title":"Application of Rough Set Theory to High Throughput Screening Data for Rational Selection of Lead Compounds","authors":"Michio Koyama, K. Hasegawa, Masamoto Arakawa, K. Funatsu","doi":"10.1273/CBIJ.8.85","DOIUrl":"https://doi.org/10.1273/CBIJ.8.85","url":null,"abstract":"In the field of drug discovery, high-throughput screening (HTS) is widely used to identify new lead compounds. A considerable number of hit compounds, however, will subsequently be found to have low activities when their inhibitory activities are measured more precisely. Such compounds are called false positives. For a more efficient selection of lead compounds, virtual screening methods with QSAR models have been investigated, but no definitive solutions have been found. In this study, we propose an effective method to identify lead compounds. The proposed method is based on rough set theory (RST), which is a mathematical tool for depicting the uncertainty and vagueness of knowledge. The essential parts of RST are the construction of reducts, which are minimal subsets of variables to distinguish samples, and the extraction of rules using their reducts. By applying RST to the QSAR study of monoamine oxidase (MAO) inhibitors, we extracted several rules for identifying lead compounds. First, 3D-structures of MAO inhibitors were generated uniformly by CORINA, and chemical descriptors were calculated by the Volsurf method. Finally, three unique rules were extracted by using RST. It is found that the each rule is chemically reasonable and compatible with previous studies. Furthermore, the predictive power of RST was also proved by comparison with partial least squares (PLS) and decision tree (DT). These results demonstrate the usefulness of our method.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":"52 1","pages":"85-95"},"PeriodicalIF":0.3,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81100203","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: 5