International Journal of Bioinformatics Research and Applications最新文献_第7页

Combining classifiers generated by multi-gene genetic programming for protein fold recognition using genetic algorithm. 结合多基因遗传规划生成的分类器进行遗传算法蛋白质折叠识别。

International Journal of Bioinformatics Research and Applications Pub Date : 2015-01-01 DOI: 10.1504/IJBRA.2015.068092

Mahshid Khatibi Bardsiri, Mahdi Eftekhari, Reza Mousavi

引用次数: 1

To study percentage distribution of target genes encoding proteins of different classes in Helicobacter pylori strain J99 and identification of potential therapeutic targets to reduce its proliferation. 目的:研究幽门螺杆菌J99中不同类别蛋白编码靶基因的百分比分布，寻找抑制其增殖的潜在治疗靶点。

International Journal of Bioinformatics Research and Applications Pub Date : 2015-01-01 DOI: 10.1504/IJBRA.2015.067335

Megha Vaidya, Hetalkumar Panchal

{"title":"To study percentage distribution of target genes encoding proteins of different classes in Helicobacter pylori strain J99 and identification of potential therapeutic targets to reduce its proliferation.","authors":"Megha Vaidya, Hetalkumar Panchal","doi":"10.1504/IJBRA.2015.067335","DOIUrl":"https://doi.org/10.1504/IJBRA.2015.067335","url":null,"abstract":"Helicobacter pylori are one of the most common bacterial pathogens in humans whose seropositivity increases with age and low socio-economic status. Due to presence of its pathogenic-island causes chronic persistent and atrophic gastritis in adults and children that often culminate in development of gastric and duodenal ulcers. Studies indicate that infected individuals have two to sixfold increased risk of developing gastric cancer and mucosal associated lymphoid tissue lymphoma compared to their uninfected counterparts. The complete genome sequences have provided a plethora of potential drug targets. Subtractive study holds the promise of providing a conceptual framework for identification of potential drug targets and providing insights to understand the biological regulatory mechanisms in diseases, which are playing an increasingly important role in searching for novel drug targets from the information contained in genomics. In this paper, we discuss subtractive study approaches for identifying drug targets, with the emphasis on the modelling of target protein and docking of the modelled protein with probable ligand by using computational tools. ","PeriodicalId":35444,"journal":{"name":"International Journal of Bioinformatics Research and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJBRA.2015.067335","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33043357","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

Artificial neural networks for dihedral angles prediction in enzyme loops: a novel approach. 酶环二面角预测的人工神经网络:一种新方法。

International Journal of Bioinformatics Research and Applications Pub Date : 2015-01-01 DOI: 10.1504/IJBRA.2015.068090

Samer I Al-Gharabli, Salem Al-Agtash, Nathir A Rawashdeh, Khaled R Barqawi

{"title":"Artificial neural networks for dihedral angles prediction in enzyme loops: a novel approach.","authors":"Samer I Al-Gharabli, Salem Al-Agtash, Nathir A Rawashdeh, Khaled R Barqawi","doi":"10.1504/IJBRA.2015.068090","DOIUrl":"https://doi.org/10.1504/IJBRA.2015.068090","url":null,"abstract":"Structure prediction of proteins is considered a limiting step and determining factor in drug development and in the introduction of new therapies. Since the 3D structures of proteins determine their functionalities, prediction of dihedral angles remains an open and important problem in bioinformatics, as well as a major step in discovering tertiary structures. This work presents a method that predicts values of the dihedral angles φ and ψ for enzyme loops based on data derived from amino acid sequences. The prediction of dihedral angles is implemented through a neural network based mining mechanism. The amino acid sequence data represents 6342 enzyme loop chains with 18,882 residues. The initial neural network input was a selection of 115 features and the outputs were the predicted dihedral angles φ and ψ. The simulation results yielded a 0.64 Pearson's correlation coefficient. After feature selection through determining insignificant features, the input feature vector size was reduced to 45, while maintaining close to identical performance. ","PeriodicalId":35444,"journal":{"name":"International Journal of Bioinformatics Research and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJBRA.2015.068090","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33018042","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: 2

Classification methods for the analysis of LH-PCR data associated with inflammatory bowel disease patients. 分类方法分析与炎症性肠病患者相关的LH-PCR数据。

International Journal of Bioinformatics Research and Applications Pub Date : 2015-01-01 DOI: 10.1504/IJBRA.2015.068087

Nuttachat Wisittipanit, Huzefa Rangwala, Masoumeh Sikaroodi, Ali Keshavarzian, Ece A Mutlu, Patrick Gillevet

引用次数: 8

Preclinical evaluation and molecular docking of 2,5-di-tert-butyl-1,4-benzoquinone (DTBBQ) from Streptomyces sp. VITVSK1 as a potent antibacterial agent. 链霉菌(Streptomyces sp. VITVSK1)中2,5-二叔丁基-1,4-苯醌(DTBBQ)的临床前评价和分子对接。

International Journal of Bioinformatics Research and Applications Pub Date : 2015-01-01 DOI: 10.1504/IJBRA.2015.068089

Vinay Gopal Jannu, Pratibha Sanjenbam, Krishnan Kannabiran

引用次数: 5

RadixHap: a radix tree-based heuristic for solving the single individual haplotyping problem. RadixHap:一个基于基数树的启发式算法，用于解决单个单倍型问题。

International Journal of Bioinformatics Research and Applications Pub Date : 2015-01-01 DOI: 10.1504/IJBRA.2015.067336

Tai-Chun Wang, Javid Taheri, Albert Y Zomaya

{"title":"RadixHap: a radix tree-based heuristic for solving the single individual haplotyping problem.","authors":"Tai-Chun Wang, Javid Taheri, Albert Y Zomaya","doi":"10.1504/IJBRA.2015.067336","DOIUrl":"https://doi.org/10.1504/IJBRA.2015.067336","url":null,"abstract":"Single nucleotide polymorphism studies have recently received significant amount of attention from researchers in many life science disciplines. Previous researches indicated that a series of SNPs from the same chromosome, called haplotype, contains more information than individual SNPs. Hence, discovering ways to reconstruct reliable Single Individual Haplotypes becomes one of the core issues in the whole-genome research nowadays. However, obtaining sequence from current high-throughput sequencing technologies always contain inevitable sequencing errors and/or missing information. The SIH reconstruction problem can be formulated as bi-partitioning the input SNP fragment matrix into paternal and maternal sections to achieve minimum error correction; a problem that is proved to be NP-hard. In this study, we introduce a greedy approach, named RadixHap, to handle data sets with high error rates. The experimental results show that RadixHap can generate highly reliable results in most cases. Furthermore, the algorithm structure of RadixHap is particularly suitable for whole-genome scale data sets. ","PeriodicalId":35444,"journal":{"name":"International Journal of Bioinformatics Research and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJBRA.2015.067336","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33043358","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

Two scenarios for overcoming drug resistance by co-targeting. 通过共同靶向克服耐药性的两种情况。

International Journal of Bioinformatics Research and Applications Pub Date : 2015-01-01 DOI: 10.1504/IJBRA.2015.067338

Golnaz Taheri, Marzieh Ayati, Limsoon Wong, Changiz Eslahchi

引用次数: 2

Looking into the genome of Thermosynechococcus elongatus (thermophilic cyanobacteria) with codon selection and usage perspective. 从密码子选择和使用的角度研究嗜热蓝藻热聚球菌的基因组。

International Journal of Bioinformatics Research and Applications Pub Date : 2015-01-01 DOI: 10.1504/IJBRA.2015.068088

Ratna Prabha, Dhananjaya P Singh, Anil Rai

{"title":"Looking into the genome of Thermosynechococcus elongatus (thermophilic cyanobacteria) with codon selection and usage perspective.","authors":"Ratna Prabha, Dhananjaya P Singh, Anil Rai","doi":"10.1504/IJBRA.2015.068088","DOIUrl":"https://doi.org/10.1504/IJBRA.2015.068088","url":null,"abstract":"Genome analysis of thermophilic cyanobacterium, Thermosynechococcus elongatus BP-1 revealed factors ruling choices of codons in this organism. Multiple parameters like Nc, GC3s, RSCU, Codon Adaptation Index (CAI), optimal and rare codons, codon-pair context and amino acid usage were analysed and compositional constraint was identified as major factor. Wide range of Nc values for the same GC3 content suggested the role of translational selection. Mutational bias is suggested at synonymous position. Among optimal codons for translation, most were GC-ending. Seven codons (AGA, AGG, AUA, UAA, UAG, UCA and UGA) were found to have least occurrence in the entire genome and except stop codons all were A-ending (exception AGG). Most widely used codon-pair in the genome are G-ending or C-ending and A-ending or U-ending codons make pair with G-ending or C-ending codons. Amino acids which are largely distributed in T. elongatus tend to use G-ending or C-ending codons most frequently. Findings showed cumulative role of translational selection, translational accuracy and gene expression levels with mutational bias as key player in codon selection pattern of this organism. ","PeriodicalId":35444,"journal":{"name":"International Journal of Bioinformatics Research and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJBRA.2015.068088","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33143605","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

PMS6: a fast algorithm for motif discovery. PMS6:一种快速的motif发现算法。

International Journal of Bioinformatics Research and Applications Pub Date : 2014-01-01 DOI: 10.1504/IJBRA.2014.062990

Shibdas Bandyopadhyay, Sartaj Sahni, Sanguthevar Rajasekaran

引用次数: 24

Editorial. 社论。

International Journal of Bioinformatics Research and Applications Pub Date : 2014-01-01

Syed N Mujahid, Dmytro Korenkevych, Panos M Pardalos

引用次数: 0