Journal of Theoretical & Computational Chemistry最新文献_第8页

Ab-initio binding of barnase–barstar with DelPhiForce steered Molecular Dynamics (DFMD) approach barnase-barstar与DelPhiForce的Ab-initio结合引导分子动力学(DFMD)方法

IF 2.4

Journal of Theoretical & Computational Chemistry Pub Date : 2020-06-01 DOI: 10.1142/s0219633620500169

Mahesh Koirala, E. Alexov

引用次数: 2

Improving the classification performance with group lasso-based ranking method in high dimensional correlated data 在高维相关数据中使用基于组套索的排序方法提高分类性能

IF 2.4

Journal of Theoretical & Computational Chemistry Pub Date : 2020-05-01 DOI: 10.1142/s021963362040009x

Abhijeet R. Patil, Bong-Jin Choi, Sangjin Kim

{"title":"Improving the classification performance with group lasso-based ranking method in high dimensional correlated data","authors":"Abhijeet R. Patil, Bong-Jin Choi, Sangjin Kim","doi":"10.1142/s021963362040009x","DOIUrl":"https://doi.org/10.1142/s021963362040009x","url":null,"abstract":"The high-throughput correlated DNA methylation (DNAmeth) dataset generated from Illumina Infinium Human Methylation 27 (IIHM 27K) BeadChip assay. In the DNAmeth data, there are several CpG sites for every gene, and these grouped CpG sites are highly correlated. Most of the current filtering-based ranking (FBR) methods do not consider the group correlation structures. Obtaining the significant features with the FBR methods and applying these features to the classifiers to attain the best classification accuracy in highly correlated DNAmeth data is a challenging task. In this research, we introduce a resampling of group least absolute shrinkage and selection operator (glasso) FBR method capable of ignoring the unrelated features in the data considering the group correlation among the features. The various classifiers, such as random forests (RF), Naive Bayes (NB), and support vector machines (SVM) with the significant CpGs obtained from the proposed resampling of group lasso-based ranking (RGLR) method helped to boost the classification accuracy. Through simulated and experimental prostate DNAmeth data, we showed that higher performance of accuracy, sensitivity, specificity, and geometric mean is achieved by ignoring the unimportant CpG sites through the RGLR method.","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2020-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/s021963362040009x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48757915","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

Binary chemical reaction with activation energy in dissipative flow of non-Newtonian nanomaterial 非牛顿纳米材料耗散流中具有活化能的二元化学反应

IF 2.4

Journal of Theoretical & Computational Chemistry Pub Date : 2020-05-01 DOI: 10.1142/s0219633620400064

M. Khan, F. Alzahrani

{"title":"Binary chemical reaction with activation energy in dissipative flow of non-Newtonian nanomaterial","authors":"M. Khan, F. Alzahrani","doi":"10.1142/s0219633620400064","DOIUrl":"https://doi.org/10.1142/s0219633620400064","url":null,"abstract":"this paper deals with the entropy optimization and heat transport of magneto-nanomaterial flow of non-newtonian (jeffrey fluid) towards a curved stretched surface. mhd fluid is accounted. the modeling of energy expression is developed subject to brownian diffusion , joule (ohmic) heating, thermophoresis and viscous dissipation . total entropy rate is discussed with the help of fluid friction irreversibility, mass transfer irreversibility, joule heating irreversibility and heat transfer irreversibility. binary chemical reaction with the smallest amount of activation energy is further considered. the governing equations of jeffrey fluid with effects of hydrodynamic, thermal radiation , heat and mass transfer were solved through built-in- shooting method . the flow variables on the entropy rate, velocity field , concentration, bejan number, skin friction coefficient and temperature are physically discussed through various graphs. the outcomes reveal that the entropy rate increases with an enhancement in curvature parameter. such obtained outcomes help in mechanical and industrial engineering sciences. moreover, the velocity and temperature decays versus ratio of relaxation to retardation times are also noticed.","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2020-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/s0219633620400064","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47385501","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: 69

A computational model of ESAT-6 complex in membrane. 膜中 ESAT-6 复合物的计算模型。

IF 2.4

Journal of Theoretical & Computational Chemistry Pub Date : 2020-05-01 Epub Date: 2020-03-17 DOI: 10.1142/s0219633620400027

Chitra Karki, Yuejiao Xian, Yixin Xie, Shengjie Sun, Alan E Lopez-Hernandez, Brenda Juarez, Jun Wang, Jianjun Sun, Lin Li

{"title":"A computational model of ESAT-6 complex in membrane.","authors":"Chitra Karki, Yuejiao Xian, Yixin Xie, Shengjie Sun, Alan E Lopez-Hernandez, Brenda Juarez, Jun Wang, Jianjun Sun, Lin Li","doi":"10.1142/s0219633620400027","DOIUrl":"10.1142/s0219633620400027","url":null,"abstract":"One quarter of the world's population are infected by Mycobacterium tuberculosis (Mtb), which is a leading death-causing bacterial pathogen. Recent evidence has demonstrated that two virulence factors, ESAT-6 and CFP-10, play crucial roles in Mtb's cytosolic translocation. Many efforts have been made to study the ESAT-6 and CFP-10 proteins. Some studies have shown that ESAT-6 has an essential role in rupturing phagosome. However, the mechanisms of how ESAT-6 interacts with the membrane have not yet been fully understood. Recent studies indicate that the ESAT-6 disassociates with CFP-10 upon their interaction with phagosome membrane, forming a membrane-spanning pore. Based on these observations, as well as the available structure of ESAT-6, ESAT-6 is hypothesized to form an oligomer for membrane insertion as well as rupturing. Such an ESAT-6 oligomer may play a significant role in the tuberculosis infection. Therefore, deeper understanding of the oligomerization of ESAT-6 will establish new directions for tuberculosis treatment. However, the structure of the oligomer of ESAT-6 is not known. Here, we proposed a comprehensive approach to model the complex structures of ESAT-6 oligomer inside a membrane. Several computational tools, including MD simulation, symmetrical docking, MM/PBSA, are used to obtain and characterize such a complex structure. Results from our studies lead to a well-supported hypothesis of the ESAT-6 oligomerization as well as the identification of essential residues in stabilizing the ESAT-6 oligomer which provide useful insights for future drug design targeting tuberculosis. The approach in this research can also be used to model and study other cross-membrane complex structures.","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2020-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8245204/pdf/nihms-1717626.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39141124","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Editorial — Special Issue on Novel Methods in Computational Chemistry and their Applications to Biological Problems: Part 1 社论-计算化学新方法及其在生物学问题上的应用:第1部分

IF 2.4

Journal of Theoretical & Computational Chemistry Pub Date : 2020-05-01 DOI: 10.1142/s0219633620020010

Lin Li

引用次数: 0

Predicting mucin-type O-Glycosylation using enhancement value products from derived protein features. 利用衍生蛋白质特征的增强值乘积预测粘蛋白型 O-糖基化。

IF 2.4

Journal of Theoretical & Computational Chemistry Pub Date : 2020-05-01 Epub Date: 2020-06-15 DOI: 10.1142/s0219633620400039

Jonathon E Mohl, Thomas Gerken, Ming-Ying Leung

{"title":"Predicting mucin-type O-Glycosylation using enhancement value products from derived protein features.","authors":"Jonathon E Mohl, Thomas Gerken, Ming-Ying Leung","doi":"10.1142/s0219633620400039","DOIUrl":"10.1142/s0219633620400039","url":null,"abstract":"Mucin-type O-glycosylation is one of the most common post-translational modifications of proteins. This glycosylation is initiated in the Golgi by the addition of the sugar N-acetylgalactosamine (GalNAc) onto protein Ser and Thr residues by a family of polypeptide GalNAc transferases. In humans there are 20 isoforms that are differentially expressed across tissues that serve multiple important biological roles. Using random peptide substrates, isoform specific amino acid preferences have been obtained in the form of enhancement values (EV). These EVs alone have previously been used to predict O-glycosylation sites via the web based ISOGlyP (Isoform Specific O-Glycosylation Prediction) tool. Here we explore additional protein features to determine whether these can complement the random peptide derived enhancement values and increase the predictive power of ISOGlyP. The inclusion of additional protein substrate features (such as secondary structure and surface accessibility) was found to increase sensitivity with minimal loss of specificity, when tested with three different published in vivo O-glycoproteomics data sets, thus increasing the overall accuracy of the ISOGlyP predictions.","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2020-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7671581/pdf/nihms-1602432.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38619236","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Theoretical evaluation of corrosion inhibition performance of six thiadiazole derivatives 六种噻二唑衍生物缓蚀性能的理论评价

IF 2.4

Journal of Theoretical & Computational Chemistry Pub Date : 2020-04-27 DOI: 10.1142/s0219633620500108

Hongfu Mi, Wenhe Wang, Yaling Liu, Taiyang Wang

引用次数: 4

Eigensolutions and theoretic quantities under the nonrelativistic wave equation 非相对论性波动方程下的本征解和理论量

IF 2.4

Journal of Theoretical & Computational Chemistry Pub Date : 2020-04-27 DOI: 10.1142/s0219633620500078

C. Onate, L. S. Adebiyi, D. T. Bankole

引用次数: 1

Computational study of reverse water gas shift reaction on Cu38 cluster model and Cu slab model Cu38簇模型和Cu板模型上逆水气转移反应的计算研究

IF 2.4

Journal of Theoretical & Computational Chemistry Pub Date : 2020-04-27 DOI: 10.1142/s021963362050008x

Dabin Qi, Luo Xudong, Jun Yao, Lu Xiaojun, Zhan Zhang

引用次数: 1

A theoretical study on cyclometalated iridium (III) complexes by using a density functional theory 用密度泛函理论研究环金属化铱(III)配合物

IF 2.4

Journal of Theoretical & Computational Chemistry Pub Date : 2020-04-14 DOI: 10.1142/s0219633620500066

S. Erkan, Duran Karakaş

引用次数: 2