In Silico Biology最新文献_第5页

Fragment-based molecular design of new competitive dengue Den2 Ns2b/Ns3 inhibitors from the components of fingerroot (Boesenbergia rotunda). 来自指根(Boesenbergia rotunda)成分的新型登革热竞争性Den2 Ns2b/Ns3抑制剂的片段分子设计

In Silico Biology Pub Date : 2011-01-01 DOI: 10.3233/ISB-2012-0442

Neni Frimayanti, Sharifuddin M Zain, Vannajan Sanghiran Lee, Habibah A Wahab, Rohana Yusof, Noorsaadah Abd Rahman

引用次数: 13

Association of antigenic properties to structure of the hepatitis C virus NS3 protein. 丙型肝炎病毒NS3蛋白抗原特性与结构的关系

In Silico Biology Pub Date : 2011-01-01 DOI: 10.3233/ISB-2012-0455

James Lara, Yury Khudyakov

引用次数: 0

Molecular modeling and docking analysis of beta-lactamases with inhibitors: a comparative study. β -内酰胺酶与抑制剂的分子建模和对接分析:一项比较研究。

In Silico Biology Pub Date : 2011-01-01 DOI: 10.3233/ISB-2012-0443

Mohd Danishuddin, Asad U Khan

{"title":"Molecular modeling and docking analysis of beta-lactamases with inhibitors: a comparative study.","authors":"Mohd Danishuddin, Asad U Khan","doi":"10.3233/ISB-2012-0443","DOIUrl":"https://doi.org/10.3233/ISB-2012-0443","url":null,"abstract":"Beta-lactamases are bacterial enzymes which impart resistance against β-lactam-antibiotics. CTX-Ms are the β-lactamases that target cephalosporin antibiotics (e.g. cefotaxime and ceftazidime) while SME-1, KPC-2, IMI-1 and SFC-1 target carbapenems. Clavulanic acid, sulbactam and tazobactam are traditional β-lactamase inhibitors while LN1-255 and NXL-104 whereas novel inhibitors, inhibiting the activity of these enzymes. Studying the binding pattern of these drugs is helpful in predicting the versatile inhibitors for betalactamases. The aims of the study were: describing the mode of interaction of CTX-M (modeled from the blaCTX-M gene of this study) and the said carbapenemases with their respective target drugs and inhibitors and to perform an in silico comparison of the efficacies of traditional and novel β-lactamase-inhibitors based on fitness score. The blaCTX-M marker was PCR-amplified from plasmid DNA of E. coli strain isolated from community-acquired urinary tract infection. E. coli C600 cells (harboring cloned blaCTX-M) were found positive for extended-spectrum-β-lactamase (ESBL) production by the double-disk-synergy test. The three dimensional structures of CTX-M-15, SME-1 and IMI-1 were predicted by Swiss Model Server. The interaction between selected structures and inhibitors was performed by GOLD 5.0. On the basis of the docking score and binding pattern, we conclude that compound LN1-255 followed by tazobactam is best inhibitor against all the selected target enzymes as compared to clavulanate, sulbactam and NXL-104. Five conserved amino acids, Ser70, Ser130, Lys235, Thr236 and Gly237 were found crucial in stabilizing the complexes through hydrogen bonding and hydrophobic interactions.","PeriodicalId":39379,"journal":{"name":"In Silico Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3233/ISB-2012-0443","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31091784","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

Computer System for Analysis of Molecular Evolution Modes (SAMEM): analysis of molecular evolution modes at deep inner branches of the phylogenetic tree. 分子进化模式分析计算机系统(SAMEM):分析系统发育树深层内部分支的分子进化模式。

In Silico Biology Pub Date : 2011-01-01 DOI: 10.3233/ISB-2012-0446

Konstantin V Gunbin, Valentin V Suslov, Mikhail A Genaev, Dmitry A Afonnikov

引用次数: 9

ANDVisio: a new tool for graphic visualization and analysis of literature mined associative gene networks in the ANDSystem. ANDVisio:一个新的工具，用于图形可视化和分析文献挖掘关联基因网络在ANDSystem。

In Silico Biology Pub Date : 2011-01-01 DOI: 10.3233/ISB-2012-0449

P S Demenkov, T V Ivanisenko, N A Kolchanov, V A Ivanisenko

引用次数: 40

Coordinated evolution among hepatitis C virus genomic sites is coupled to host factors and resistance to interferon. 丙型肝炎病毒基因组位点之间的协调进化与宿主因子和对干扰素的耐药性有关。

In Silico Biology Pub Date : 2011-01-01 DOI: 10.3233/ISB-2012-0456

James Lara, John E Tavis, Maureen J Donlin, William M Lee, He-Jun Yuan, Brian L Pearlman, Gilberto Vaughan, Joseph C Forbi, Guo-Liang Xia, Yury E Khudyakov

引用次数: 16

GO for integration of expression data. GO用于表达式数据的集成。

In Silico Biology Pub Date : 2011-01-01 DOI: 10.3233/ISB-2012-0439

Dikla Dotan-Cohen, Dana Moonshine, Moshe Natan, Yonat Shemer-Avni, Avraham A Melkman

{"title":"GO for integration of expression data.","authors":"Dikla Dotan-Cohen, Dana Moonshine, Moshe Natan, Yonat Shemer-Avni, Avraham A Melkman","doi":"10.3233/ISB-2012-0439","DOIUrl":"https://doi.org/10.3233/ISB-2012-0439","url":null,"abstract":"The low reproducibility of differential expression of individual genes in microarray experiments has led to the suggestion that experiments be analyzed in terms of gene characteristics, such as GO categories or pathways, in order to enhance the robustness of the results. An implicit assumption of this approach is that the different experiments in effect randomly sample the genes participating in an active process. We argue that by the same rationale it is possible to perform this higher-level analysis on the aggregation of genes that are differentially-expressed in different expression-based studies, even if the experiments used different platforms. The aggregation increases the reliability of the results, it has the potential for uncovering signals that are liable to escape detection in the individual experiments, and it enables a more thorough mining of the ever more plentiful microarray data. We present here a proof-of-concept study of these ideas, using ten studies describing the changes in expression profiles of human host genes in response to infection by Retroviridae or Herpesviridae viral families. We supply a tool (accessible at www.cs.bgu.ac.il/∼waytogo) which enables the user to learn about genes and processes of interest in this study.","PeriodicalId":39379,"journal":{"name":"In Silico Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3233/ISB-2012-0439","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30550459","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

Illuminator: increasing synergies between medicinal and computational chemists. 启发:增加药物和计算化学家之间的协同作用。

In Silico Biology Pub Date : 2011-01-01 DOI: 10.3233/CI-2009-0017

Alberto Gobbi, Matthew Lardy, Sun Hee Kim, Frank Ruebsam, Martin Tran, Stephen E Webber, Alan X Xiang

引用次数: 1

Obituary. 讣告。

In Silico Biology Pub Date : 2011-01-01 DOI: 10.3233/ISB-2012-0450

J E van den Ende

引用次数: 0

Haploid evolutionary constructor: new features and further challenges. 单倍体进化构造:新特征和进一步挑战。

In Silico Biology Pub Date : 2011-01-01 DOI: 10.3233/ISB-2012-0447

Sergey A Lashin, Yury G Matushkin

引用次数: 9