Chem-Bio Informatics Journal最新文献_第8页

遺伝子ネットワークのS-systemモデル同定のための効率的パラメータ推定：さらなる問題分割と交互最適化法の提案基因网络的S-system模型鉴定的有效参数估计:提出进一步的问题分割和交互优化方法

IF 0.3

Chem-Bio Informatics Journal Pub Date : 2011-01-01 DOI: 10.1273/CBIJ.11.24

周平木村, 幸輝松村, 岡田眞里子

{"title":"遺伝子ネットワークのS-systemモデル同定のための効率的パラメータ推定：さらなる問題分割と交互最適化法の提案","authors":"周平木村, 幸輝松村, 岡田眞里子","doi":"10.1273/CBIJ.11.24","DOIUrl":"https://doi.org/10.1273/CBIJ.11.24","url":null,"abstract":"The problem decomposition strategy is a very efficient technique for the inference of S-system models of genetic networks. This strategy defines the inference of a genetic network consisting of N genes as N subproblems, each of which is a 2(N+1)-dimensional function optimization problem. Genetic networks made up of dozens genes can be analyzed with this strategy, though the computational cost in doing so remains quite high. In this study, we attempt to infer S-system models more efficiently by further dividing each 2(N+1)-dimensional subproblem into one (N+2)-dimensional problem and one (N+1)-dimensional problem. The subproblems are divided using the genetic network inference method based on linear programming machines (LPMs). Next, we propose a new method for estimating the S-system parameters by alternately solving the two divided problems. According to our experimental results, the proposed approach requires less than one-third of the time required by the original problem decomposition approach. Finally, we apply our approach to actual expression data from the bacterial SOS DNA repair system.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":null,"pages":null},"PeriodicalIF":0.3,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74908362","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

Discovery of Novel Antimicrobial Agents Targeting the Bacterial RNA Polymerase by High-Throughput Virtual Screening 利用高通量虚拟筛选技术发现靶向细菌RNA聚合酶的新型抗菌药物

IF 0.3

Chem-Bio Informatics Journal Pub Date : 2011-01-01 DOI: 10.1273/CBIJ.11.52

K. Onodera, T. Kawasaki, S. Kamijo

引用次数: 1

Comparison of binding affinity evaluations for FKBP ligands with state-of-the-art computational methods: FMO, QM/MM, MM-PB/SA and MP-CAFEE approaches FMO、QM/MM、MM- pb /SA和MP-CAFEE方法对FKBP配体结合亲和力评价的比较

IF 0.3

Chem-Bio Informatics Journal Pub Date : 2010-01-01 DOI: 10.1273/CBIJ.10.32

博文渡邉, 成典田中, 憲明沖本, 亜樹長谷川, 泰地真弘人, 義明谷田, 崇志三井, 勝山マリコ, 秀章藤谷

引用次数: 12

Comprehensive In silico Analysis of the Expression of Glycogenes in Breast Cancer 乳腺癌中糖基因表达的计算机综合分析

IF 0.3

Chem-Bio Informatics Journal Pub Date : 2010-01-01 DOI: 10.1273/CBIJ.10.100

H. Kojo, Atsushi Doi, Y. Eguchi, T. Miyagishima, T. Taki, K. Makino, H. Terada

{"title":"Comprehensive In silico Analysis of the Expression of Glycogenes in Breast Cancer","authors":"H. Kojo, Atsushi Doi, Y. Eguchi, T. Miyagishima, T. Taki, K. Makino, H. Terada","doi":"10.1273/CBIJ.10.100","DOIUrl":"https://doi.org/10.1273/CBIJ.10.100","url":null,"abstract":"To elucidate the role of alterations to carbohydrate chains in cancer, we investigated changes in the expression of 107 glycogenes with the onset and progression of breast cancer by conducting an in silico analysis using GEO-registered data. A comparison between 43 breast tumors and paired normal controls (GSE15852) revealed significant changes in the expression of 24 glycogenes including the genes for 5 N-acetylgalactosaminyltransferases, 3 nucleotide sugar transporters, 3 asparagine-linked glycosylation-involved enzymes, 2 N-acetylglucosaminyl transferases, 2 fucosyltransferases, 2 sulfotransferases, 2 sulfatases, 1 glycosaminoglycan synthesis-involved enzyme, 1 glycosyltransferase, 1 glucosyltransferase, 1 sialyltransferase, and 1 N-acetylglucosaminidase. Furthermore, to clarify whether the expression of particular glycogenes changed dependent on the stage of cancer, we compared gene expression between preinvasive and invasive ductal carcinomas (GDS2045). The expression of 6 glycogenes exhibited significant changes in GDS2045. Notably, 3 of these genes were related to the sulfonation of carbohydrate chains. The upand down-regulated glycogenes were related to the synthesis of carbohydrate chains and the effects of changes in the expression of glycogenes on oncogenesis were discussed.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":null,"pages":null},"PeriodicalIF":0.3,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76772754","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

Gene expression informatics with an automatic histogram-type membership function for non-uniform data 具有非均匀数据自动直方图型隶属函数的基因表达信息学

IF 0.3

Chem-Bio Informatics Journal Pub Date : 2010-01-01 DOI: 10.1273/CBIJ.10.13

Akito Daiba, S. Ito, Tsutomu Takeuchi, M. Yohda

引用次数: 0

SOSUImp1: high performance prediction system for single-spanning membrane proteins SOSUImp1:单跨膜蛋白的高性能预测系统

IF 0.3

Chem-Bio Informatics Journal Pub Date : 2010-01-01 DOI: 10.1273/CBIJ.10.E_2

T. Tsuji, F. Akazawa, Ryusuke Sawada, S. Mitaku

{"title":"SOSUImp1: high performance prediction system for single-spanning membrane proteins","authors":"T. Tsuji, F. Akazawa, Ryusuke Sawada, S. Mitaku","doi":"10.1273/CBIJ.10.E_2","DOIUrl":"https://doi.org/10.1273/CBIJ.10.E_2","url":null,"abstract":"Single-spanning membrane proteins (MP1) occupy the largest component of membrane proteins in total open reading frames of organisms, having essential functions such as signal transduction, immunological reaction and cell adhesion. We developed a novel software system comprised of two filtering layers for predicting MP1 with or without a signal peptide region. In the first filtering layer, we selected membrane proteins with one or two transmembrane (TM) regions by the membrane protein prediction system SOSUI, which is accurate in predicting transmembrane regions but cannot identify signal peptide regions. The second filtering layer was comprised of several modules for distinguishing signal peptide regions. On the assumption that a signal peptide has two kinds of sequences at the N-terminus by which the signal peptide is embedded into membrane and cleaved at its C-terminal end, we calculated two discrimination scores by the canonical discriminant analysis, using averages of several physical properties around the first N-terminal hydrophobic cluster. This prediction system SOSUImp1 comprised of two filtering layers could discriminate very accurately among five types of proteins: cytoplasmic soluble proteins and secretory proteins, MP1 with and without a signal peptide, and multi spanning membrane proteins. The performance for MP1 with a signal peptide that is important in the cell-cell communication was particularly high compared with previous prediction systems.The prediction system SOSUImp1 and the dataset of 5932 proteins used for developing the system are available at http://bp.nuap.nagoya-u.ac.jp/sosui/mp1/","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":null,"pages":null},"PeriodicalIF":0.3,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73441956","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

Acceleration of monomer self-consistent charge process in fragment molecular orbital method 片段分子轨道法加速单体自洽电荷过程

IF 0.3

Chem-Bio Informatics Journal Pub Date : 2010-01-01 DOI: 10.1273/CBIJ.10.24

Takeshi Ishikawa, K. Kuwata

引用次数: 0

GSK-3β 阻害剤のイン・シリコドッキングスタディーおよびリガンドデザイン sk -3β抑制剂的incilico对接研究及配体设计

IF 0.3

Chem-Bio Informatics Journal Pub Date : 2010-01-01 DOI: 10.1273/CBIJ.10.1

P. BabuAjay, Chitti Sashikanth, B. Rajesh, Prasanth Vishnu, Kishen Radha Jv, R. ValiKhadar

引用次数: 5

Discovery of novel anti-proliferative compounds against A549 cells by virtual screening 通过虚拟筛选发现抗A549细胞增殖的新化合物

IF 0.3

Chem-Bio Informatics Journal Pub Date : 2010-01-01 DOI: 10.1273/CBIJ.10.46

P. A. Babu, P. A. Babu, M. Narasu, SRINIVAS KOLLI

{"title":"Discovery of novel anti-proliferative compounds against A549 cells by virtual screening","authors":"P. A. Babu, P. A. Babu, M. Narasu, SRINIVAS KOLLI","doi":"10.1273/CBIJ.10.46","DOIUrl":"https://doi.org/10.1273/CBIJ.10.46","url":null,"abstract":"CDK2 (Cyclin Dependent Kinase 2) acts as a potential therapeutic target in cancer and several efforts have been made to find more specific, potent and selective ATP competitive CDK2 inhibitors. In this paper, we report a virtual screening approach that resulted in 54,558 Lipinski compliant hits from ZINC database based on the features exhibited by four compounds from our previous study. Docking and scoring of all compounds using GOLD (Genetic Optimisation for Ligand Docking) software, to evaluate the affinity of binding towards CDK2 enzyme 2UZO resulted in dock scores between 41.71 - 82.33 kcal/mol. The resultant dataset of 392 hits were filtered based on the specificity between CDK2 and GSK-3β (Glycogen Synthase Kinase-3β) to obtain 17 compounds that are more specific towards CDK2. Further, re-scoring of 17 best docked poses followed by a consensus scoring approach tested with five different scoring functions such as GOLD score, CHEM score implemented in GOLD 3.1, eHiTS_score (electronic High Throughput Screening), MolDock score of Molegro software and X-Score retrieved top hits. Finally, the top ten compounds were examined for anti-proliferative effects against human lung adenocarcinoma epithelial cell line, A549 using MTT assay.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":null,"pages":null},"PeriodicalIF":0.3,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85067292","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

De novo Based Ligand generation and Docking studies of PPARδ Agonists: Correlations between Predicted Biological activity vs. Biopharmaceutical Descriptors PPARδ激动剂的从头生成和对接研究:预测生物活性与生物制药描述符之间的相关性

IF 0.3

Chem-Bio Informatics Journal Pub Date : 2010-01-01 DOI: 10.1273/CBIJ.10.74

V. Avupati, P. N. Kurre, Santoshi Rupa Bagadi, Murali Krishna Kumar Muthyala, R. Yejella

{"title":"De novo Based Ligand generation and Docking studies of PPARδ Agonists: Correlations between Predicted Biological activity vs. Biopharmaceutical Descriptors","authors":"V. Avupati, P. N. Kurre, Santoshi Rupa Bagadi, Murali Krishna Kumar Muthyala, R. Yejella","doi":"10.1273/CBIJ.10.74","DOIUrl":"https://doi.org/10.1273/CBIJ.10.74","url":null,"abstract":"Molecular docking was performed on a series of bisaryl substituted thiazoles and oxazoles as PPARδ agonists. The docking technique was applied to dock a set of representative compounds within the active site region of 3D5F using Molegro Virtual Docker v 4.0.0. For these compounds, the correlation between binding free energy (kcal/mol) and log (1/EC50) values produces a good correlation coefficient (r2 = 0.719). The docking simulation clearly predicted the binding mode that is nearly similar to the crystallographic binding mode within 0.91A RMSD. Based on the validations and interactions made by Ar1 and Ar2 substituents, ligand design was initiated considering simple combinations. For the designed compounds biopharmaceutical properties e.g. Lipophilicity (logP), Solubility (logS), Ionization constant (pKa), Distribution coefficient (logD) are predicted computationally using ACD/ChemSketch v 12.0. The hydrogen bond interactions are examined and bivariate statistical correlation between predicted biological activity (log (1/EC50) and biopharmaceutical properties are considered for evaluation. Ligand 11 (cC) thus, showed high binding energy (-206.73 kcal/mol) against PPARδ. The results avail to understand the type of interactions that occur between designed ligands with PPARδ binding site region and explain the importance of Ar1 and Ar2 substitutions on derivatives of bisaryl substituted thiazoles and oxazoles.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":null,"pages":null},"PeriodicalIF":0.3,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79764494","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: 10