Advances and Applications in Bioinformatics and Chemistry最新文献_第7页

Insights into the classification of small GTPases. 小gtpase分类的新见解。

Advances and Applications in Bioinformatics and Chemistry Pub Date : 2010-01-01 Epub Date: 2010-05-21 DOI: 10.2147/aabc.s8891

Dominik Heider, Sascha Hauke, Martin Pyka, Daniel Kessler

{"title":"Insights into the classification of small GTPases.","authors":"Dominik Heider, Sascha Hauke, Martin Pyka, Daniel Kessler","doi":"10.2147/aabc.s8891","DOIUrl":"https://doi.org/10.2147/aabc.s8891","url":null,"abstract":"In this study we used a Random Forest-based approach for an assignment of small guanosine triphosphate proteins (GTPases) to specific subgroups. Small GTPases represent an important functional group of proteins that serve as molecular switches in a wide range of fundamental cellular processes, including intracellular transport, movement and signaling events. These proteins have further gained a special emphasis in cancer research, because within the last decades a huge variety of small GTPases from different subgroups could be related to the development of all types of tumors. Using a random forest approach, we were able to identify the most important amino acid positions for the classification process within the small GTPases superfamily and its subgroups. These positions are in line with the results of earlier studies and have been shown to be the essential elements for the different functionalities of the GTPase families. Furthermore, we provide an accurate and reliable software tool (GTPasePred) to identify potential novel GTPases and demonstrate its application to genome sequences.","PeriodicalId":53584,"journal":{"name":"Advances and Applications in Bioinformatics and Chemistry","volume":"3 ","pages":"15-24"},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2147/aabc.s8891","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30143025","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: 20

Molecular biocoding of insulin. 胰岛素的分子生物学编码。

Advances and Applications in Bioinformatics and Chemistry Pub Date : 2010-01-01 Epub Date: 2010-07-28 DOI: 10.2147/aabc.s9994

Lutvo Kurić

{"title":"Molecular biocoding of insulin.","authors":"Lutvo Kurić","doi":"10.2147/aabc.s9994","DOIUrl":"https://doi.org/10.2147/aabc.s9994","url":null,"abstract":"This paper discusses cyberinformation studies of the amino acid composition of insulin, in particular the identification of scientific terminology that could describe this phenomenon, ie, the study of genetic information, as well as the relationship between the genetic language of proteins and theoretical aspects of this system and cybernetics. The results of this research show that there is a matrix code for insulin. It also shows that the coding system within the amino acid language gives detailed information, not only on the amino acid \"record\", but also on its structure, configuration, and various shapes. The issue of the existence of an insulin code and coding of the individual structural elements of this protein are discussed. Answers to the following questions are sought. Does the matrix mechanism for biosynthesis of this protein function within the law of the general theory of information systems, and what is the significance of this for understanding the genetic language of insulin? What is the essence of existence and functioning of this language? Is the genetic information characterized only by biochemical principles or it is also characterized by cyberinformation principles? The potential effects of physical and chemical, as well as cybernetic and information principles, on the biochemical basis of insulin are also investigated. This paper discusses new methods for developing genetic technologies, in particular more advanced digital technology based on programming, cybernetics, and informational laws and systems, and how this new technology could be useful in medicine, bioinformatics, genetics, biochemistry, and other natural sciences.","PeriodicalId":53584,"journal":{"name":"Advances and Applications in Bioinformatics and Chemistry","volume":"3 ","pages":"45-58"},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2147/aabc.s9994","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30143028","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: 1

Construction of random perfect phylogeny matrix. 随机完美系统发育矩阵的构建。

Advances and Applications in Bioinformatics and Chemistry Pub Date : 2010-01-01 Epub Date: 2010-11-16 DOI: 10.2147/AABC.S13397

Mehdi Sadeghi, Hamid Pezeshk, Changiz Eslahchi, Sara Ahmadian, Sepideh Mah Abadi

引用次数: 0

Simultaneous use of solution, solid-state NMR and X-ray crystallography to study the conformational landscape of the Crh protein during oligomerization and crystallization. 同时使用溶液、固态核磁共振和x射线晶体学来研究Crh蛋白在寡聚和结晶过程中的构象景观。

Advances and Applications in Bioinformatics and Chemistry Pub Date : 2010-01-01 Epub Date: 2010-06-09 DOI: 10.2147/aabc.s8715

Benjamin Bardiaux, Adrien Favier, Manuel Etzkorn, Marc Baldus, Anja Böckmann, Michael Nilges, Thérèse E Malliavin

{"title":"Simultaneous use of solution, solid-state NMR and X-ray crystallography to study the conformational landscape of the Crh protein during oligomerization and crystallization.","authors":"Benjamin Bardiaux, Adrien Favier, Manuel Etzkorn, Marc Baldus, Anja Böckmann, Michael Nilges, Thérèse E Malliavin","doi":"10.2147/aabc.s8715","DOIUrl":"https://doi.org/10.2147/aabc.s8715","url":null,"abstract":"We explore, using the Crh protein dimer as a model, how information from solution NMR, solid-state NMR and X-ray crystallography can be combined using structural bioinformatics methods, in order to get insights into the transition from solution to crystal. Using solid-state NMR chemical shifts, we filtered intra-monomer NMR distance restraints in order to keep only the restraints valid in the solid state. These filtered restraints were added to solid-state NMR restraints recorded on the dimer state to sample the conformational landscape explored during the oligomerization process. The use of non-crystallographic symmetries then permitted the extraction of converged conformers subsets. Ensembles of NMR and crystallographic conformers calculated independently display similar variability in monomer orientation, which supports a funnel shape for the conformational space explored during the solution-crystal transition. Insights into alternative conformations possibly sampled during oligomerization were obtained by analyzing the relative orientation of the two monomers, according to the restraint precision. Molecular dynamics simulations of Crh confirmed the tendencies observed in NMR conformers, as a paradoxical increase of the distance between the two β1a strands, when the structure gets closer to the crystallographic structure, and the role of water bridges in this context.","PeriodicalId":53584,"journal":{"name":"Advances and Applications in Bioinformatics and Chemistry","volume":"3 ","pages":"25-38"},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2147/aabc.s8715","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30143026","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

Pharmacogenomics of drug efficacy in the interferon treatment of chronic hepatitis C using classification algorithms. 干扰素治疗慢性丙型肝炎疗效的药物基因组学分类算法。

Advances and Applications in Bioinformatics and Chemistry Pub Date : 2010-01-01 Epub Date: 2010-06-15 DOI: 10.2147/aabc.s8656

Wan-Sheng Ke, Yuchi Hwang, Eugene Lin

{"title":"Pharmacogenomics of drug efficacy in the interferon treatment of chronic hepatitis C using classification algorithms.","authors":"Wan-Sheng Ke, Yuchi Hwang, Eugene Lin","doi":"10.2147/aabc.s8656","DOIUrl":"https://doi.org/10.2147/aabc.s8656","url":null,"abstract":"Chronic hepatitis C (CHC) patients often stop pursuing interferon-alfa and ribavirin (IFN-alfa/RBV) treatment because of the high cost and associated adverse effects. It is highly desirable, both clinically and economically, to establish tools to distinguish responders from nonresponders and to predict possible outcomes of the IFN-alfa/RBV treatments. Single nucleotide polymorphisms (SNPs) can be used to understand the relationship between genetic inheritance and IFN-alfa/RBV therapeutic response. The aim in this study was to establish a predictive model based on a pharmacogenomic approach. Our study population comprised Taiwanese patients with CHC who were recruited from multiple sites in Taiwan. The genotyping data was generated in the high-throughput genomics lab of Vita Genomics, Inc. With the wrapper-based feature selection approach, we employed multilayer feedforward neural network (MFNN) and logistic regression as a basis for comparisons. Our data revealed that the MFNN models were superior to the logistic regression model. The MFNN approach provides an efficient way to develop a tool for distinguishing responders from nonresponders prior to treatments. Our preliminary results demonstrated that the MFNN algorithm is effective for deriving models for pharmacogenomics studies and for providing the link from clinical factors such as SNPs to the responsiveness of IFN-alfa/RBV in clinical association studies in pharmacogenomics.","PeriodicalId":53584,"journal":{"name":"Advances and Applications in Bioinformatics and Chemistry","volume":"3 ","pages":"39-44"},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2147/aabc.s8656","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30143027","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: 24

Classification of heterodimer interfaces using docking models and construction of scoring functions for the complex structure prediction. 基于对接模型的异源二聚体界面分类及复杂结构预测的评分函数构建。

Advances and Applications in Bioinformatics and Chemistry Pub Date : 2009-01-01 Epub Date: 2009-09-22 DOI: 10.2147/aabc.s6347

Yuko Tsuchiya, Eiji Kanamori, Haruki Nakamura, Kengo Kinoshita

{"title":"Classification of heterodimer interfaces using docking models and construction of scoring functions for the complex structure prediction.","authors":"Yuko Tsuchiya, Eiji Kanamori, Haruki Nakamura, Kengo Kinoshita","doi":"10.2147/aabc.s6347","DOIUrl":"https://doi.org/10.2147/aabc.s6347","url":null,"abstract":"Protein-protein docking simulations can provide the predicted complex structural models. In a docking simulation, several putative structural models are selected by scoring functions from an ensemble of many complex models. Scoring functions based on statistical analyses of heterodimers are usually designed to select the complex model with the most abundant interaction mode found among the known complexes, as the correct model. However, because the formation schemes of heterodimers are extremely diverse, a single scoring function does not seem to be sufficient to describe the fitness of the predicted models other than the most abundant interaction mode. Thus, it is necessary to classify the heterodimers in terms of their individual interaction modes, and then to construct multiple scoring functions for each heterodimer type. In this study, we constructed the classification method of heterodimers based on the discriminative characters between near-native and decoy models, which were found in the comparison of the interfaces in terms of the complementarities for the hydrophobicity, the electrostatic potential and the shape. Consequently, we found four heterodimer clusters, and then constructed the multiple scoring functions, each of which was optimized for each cluster. Our multiple scoring functions were applied to the predictions in the unbound docking.","PeriodicalId":53584,"journal":{"name":"Advances and Applications in Bioinformatics and Chemistry","volume":"2 ","pages":"79-100"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2147/aabc.s6347","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30142066","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: 2

A gene expression ratio-based diagnostic test for bladder cancer. 基于基因表达比的膀胱癌诊断试验。

Advances and Applications in Bioinformatics and Chemistry Pub Date : 2009-01-01 Epub Date: 2009-01-12 DOI: 10.2147/aabc.s4148

Lingsheng Dong, Andrew J Bard, William G Richards, Matthew D Nitz, Dan Theodorescu, Raphael Bueno, Gavin J Gordon

{"title":"A gene expression ratio-based diagnostic test for bladder cancer.","authors":"Lingsheng Dong, Andrew J Bard, William G Richards, Matthew D Nitz, Dan Theodorescu, Raphael Bueno, Gavin J Gordon","doi":"10.2147/aabc.s4148","DOIUrl":"https://doi.org/10.2147/aabc.s4148","url":null,"abstract":"Purpose: Bladder cancer is relatively common but early detection techniques such as cystoscopy and cytology are somewhat limited. We developed a broadly applicable, platform-independent and clinically relevant method based on simple ratios of gene expression to diagnose human cancers. In this study, we sought to determine whether this technique could be applied to the diagnosis of bladder cancer.Experimental design: We developed a model for the diagnosis of bladder cancer using expression profiling data from 80 normal and tumor bladder tissues to identify statistically significant discriminating genes with reciprocal average expression levels in each tissue type. The expression levels of select genes were used to calculate individual gene pair expression ratios in order to assign diagnosis. The optimal model was examined in two additional published microarray data sets and using quantitative RT-PCR in a cohort of 13 frozen benign bladder urothelium samples and 13 bladder cancer samples from our institution.Results: A five-ratio test utilizing six genes proved to be 100% accurate (26 of 26 samples) for distinguishing benign from malignant bladder tissue samples (P < 10(-6)).Conclusions: : We have provided a proof of principle study for the use of gene expression ratios in the diagnosis of bladder cancer. This technique may ultimately prove to be a useful adjunct to cytopathology in screening urine specimens for bladder cancer.","PeriodicalId":53584,"journal":{"name":"Advances and Applications in Bioinformatics and Chemistry","volume":"2 ","pages":"17-22"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2147/aabc.s4148","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30142651","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: 7

On calculating the probability of a set of orthologous sequences. 计算一组同源序列的概率。

Advances and Applications in Bioinformatics and Chemistry Pub Date : 2009-01-01 Epub Date: 2009-02-26 DOI: 10.2147/aabc.s4616

Junfeng Liu, Liang Chen, Hongyu Zhao, Dirk F Moore, Yong Lin, Weichung Joe Shih

引用次数: 0

Performance of PLS regression coefficients in selecting variables for each response of a multivariate PLS for omics-type data. PLS回归系数在为组学类型数据的多变量PLS的每个响应选择变量时的表现。

Advances and Applications in Bioinformatics and Chemistry Pub Date : 2009-01-01 Epub Date: 2009-05-13 DOI: 10.2147/aabc.s3619

Giuseppe Palermo, Paolo Piraino, Hans-Dieter Zucht

{"title":"Performance of PLS regression coefficients in selecting variables for each response of a multivariate PLS for omics-type data.","authors":"Giuseppe Palermo, Paolo Piraino, Hans-Dieter Zucht","doi":"10.2147/aabc.s3619","DOIUrl":"https://doi.org/10.2147/aabc.s3619","url":null,"abstract":"Multivariate partial least square (PLS) regression allows the modeling of complex biological events, by considering different factors at the same time. It is unaffected by data collinearity, representing a valuable method for modeling high-dimensional biological data (as derived from genomics, proteomics and peptidomics). In presence of multiple responses, it is of particular interest how to appropriately \"dissect\" the model, to reveal the importance of single attributes with regard to individual responses (for example, variable selection). In this paper, performances of multivariate PLS regression coefficients, in selecting relevant predictors for different responses in omics-type of data, were investigated by means of a receiver operating characteristic (ROC) analysis. For this purpose, simulated data, mimicking the covariance structures of microarray and liquid chromatography mass spectrometric data, were used to generate matrices of predictors and responses. The relevant predictors were set a priori. The influences of noise, the source of data with different covariance structure and the size of relevant predictors were investigated. Results demonstrate the applicability of PLS regression coefficients in selecting variables for each response of a multivariate PLS, in omics-type of data. Comparisons with other feature selection methods, such as variable importance in the projection scores, principal component regression, and least absolute shrinkage and selection operator regression were also provided.","PeriodicalId":53584,"journal":{"name":"Advances and Applications in Bioinformatics and Chemistry","volume":"2 ","pages":"57-70"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2147/aabc.s3619","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30142064","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: 106

An online conserved SSR discovery through cross-species comparison. 通过跨物种比较发现在线保守SSR。

Advances and Applications in Bioinformatics and Chemistry Pub Date : 2009-01-01 Epub Date: 2009-02-08 DOI: 10.2147/aabc.s4744

Tun-Wen Pai, Chien-Ming Chen, Meng-Chang Hsiao, Ronshan Cheng, Wen-Shyong Tzou, Chin-Hua Hu

引用次数: 8