Int. J. Bioinform. Res. Appl.最新文献_第8页

Insilco new aspects of peptide-based vaccine designing for human papilloma virus infection 人乳头瘤病毒感染肽基疫苗设计的新进展

Int. J. Bioinform. Res. Appl. Pub Date : 2017-08-23 DOI: 10.1504/IJBRA.2017.10006936

Maryam Moazami-goodarzi, R. Fotouhi-Ardakani, Ali Afgar

引用次数: 1

Protein interaction based features' extraction 基于蛋白质相互作用的特征提取

Int. J. Bioinform. Res. Appl. Pub Date : 2017-08-23 DOI: 10.1504/IJBRA.2017.10006935

I. Alsmadi, S. Bettayeb

引用次数: 0

In silico identification of vaccine candidate from various screening methods against hepatitis C virus 丙型肝炎病毒不同筛选方法候选疫苗的计算机鉴定

Int. J. Bioinform. Res. Appl. Pub Date : 2017-08-23 DOI: 10.1504/IJBRA.2017.10006971

V. Kaushik, Nidhi Sharma, Joginder Singh

{"title":"In silico identification of vaccine candidate from various screening methods against hepatitis C virus","authors":"V. Kaushik, Nidhi Sharma, Joginder Singh","doi":"10.1504/IJBRA.2017.10006971","DOIUrl":"https://doi.org/10.1504/IJBRA.2017.10006971","url":null,"abstract":"Hepatitis C virus (HCV) being an infectious disease is prevalent in most parts of the world. Till date, no vaccine is being developed in the market for HCV. This paper focuses mainly on developing a peptide-based vaccine against HCV. The purpose for this study is taken to determine the suitable epitope with the help of Bioinformatics tools developed for designing a vaccine against infectious diseases such as HCV. In present work, T-cell epitope is taken into consideration, as it recognises the antigen that helps to generate peptide with the help of antigen presenting cell. With respect to T-cell epitope selection, high binding energy must be required for binding major histocompatibility complex molecule. Moreover, T-cell epitope were considered on the basis of conserved site, protease cleavage site, motif, as well as an excellent hydrophobic binding pocket with a high half-life of dissociation. In consideration to the mentioned criteria, the required bioinformatics tools are used which are designed to predict the epitopes from different envelope and non-structural proteins of HCV virus. On an average, 1,000 epitopes from various databases and tools were extracted, from which 11 adept epitopes were withdrawn virtually with a base of binding energy using MHC I and II molecule protein interaction. The best epitope predicted during study was IMYAPTIWV peptide of NS5A protein. The T-cell predicted epitope can be further used for later chore in vaccine discovery for HCV.","PeriodicalId":434900,"journal":{"name":"Int. J. Bioinform. Res. Appl.","volume":"4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130255575","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

Modelling and receptor-based virtual screening studies of GPR139 GPR139的建模和基于受体的虚拟筛选研究

Int. J. Bioinform. Res. Appl. Pub Date : 2017-08-23 DOI: 10.1504/IJBRA.2017.10006939

A. Kaushik, S. Sahi

{"title":"Modelling and receptor-based virtual screening studies of GPR139","authors":"A. Kaushik, S. Sahi","doi":"10.1504/IJBRA.2017.10006939","DOIUrl":"https://doi.org/10.1504/IJBRA.2017.10006939","url":null,"abstract":"GPR139 belongs to Class A of GPCRs family and plays key role in molecular signalling through activation of receptors and promotes exchange of Guanosine Di-phosphate (GDP) to Guanosine Tri-phosphate (GTP). GPR139 is specifically involved in neuropeptide signalling pathway, phospholipase C-activating G-protein-coupled receptor signalling pathway and is coupled to IP3 second messenger (phospholipase C activating). In this article, we report 3D structure prediction of GPR139 using threading and ab initio methods. The models were validated and optimised. Molecular dynamics simulation of GPR139 was performed for 300 ns to investigate the dynamic perturbations in predicted model, particularly variations in seven transmembrane domains and active site residues. The active site residues were identified and the 3D model was screened against large databases of chemical libraries for identification of potential lead compounds which could bind to GPR139 receptor and activate signal transduction. The screened compounds were further refined through free binding energy calculations (ΔGbind) using generalised born and surface area continuum solvation for estimating ligand-binding affinities to GPR139.","PeriodicalId":434900,"journal":{"name":"Int. J. Bioinform. Res. Appl.","volume":"2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121400213","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

Extensive computational analysis of chromosome 11 11号染色体的广泛计算分析

Int. J. Bioinform. Res. Appl. Pub Date : 2017-08-23 DOI: 10.1504/IJBRA.2017.10006938

Abhivyakti Srivastava, Mottadi Shiva, P. Kumari, Y. Hasija

引用次数: 0

Analysis for biological network properties of Alzheimer's disease associated gene set by enrichment and topological examinations 通过富集和拓扑检测分析阿尔茨海默病相关基因集的生物学网络特性

Int. J. Bioinform. Res. Appl. Pub Date : 2017-08-23 DOI: 10.1504/IJBRA.2017.10006803

Ashwani Kumar, T. Singh

引用次数: 2

Association of claudin family protein in human cancer types: a network approach claudin家族蛋白在人类癌症类型中的关联:一种网络方法

Int. J. Bioinform. Res. Appl. Pub Date : 2017-03-24 DOI: 10.1504/IJBRA.2017.10003487

M. Rambabu, J. F. P. Dass, S. Jayanthi

引用次数: 1

EhPPTome: Entamoeba histolytica protein phosphotome database EhPPTome:溶组织内阿米巴蛋白磷基因数据库

Int. J. Bioinform. Res. Appl. Pub Date : 2017-03-24 DOI: 10.1504/IJBRA.2017.10003491

Tamanna Anwar, S. Gourinath

引用次数: 3

BiETopti: biclustering ensemble technique using optimisation BiETopti:使用优化的双聚类集成技术

Int. J. Bioinform. Res. Appl. Pub Date : 2017-03-24 DOI: 10.1504/IJBRA.2017.10003485

Geeta Aggarwal, Neelima Gupta

引用次数: 0

A new and efficient method based on syntactic dependency relations features for ad hoc clinical question classification 基于句法依赖关系特征的特殊临床问题分类新方法

Int. J. Bioinform. Res. Appl. Pub Date : 2017-03-24 DOI: 10.1504/IJBRA.2017.10003490

Mourad Sarrouti, Abdelmonaime Lachkar

{"title":"A new and efficient method based on syntactic dependency relations features for ad hoc clinical question classification","authors":"Mourad Sarrouti, Abdelmonaime Lachkar","doi":"10.1504/IJBRA.2017.10003490","DOIUrl":"https://doi.org/10.1504/IJBRA.2017.10003490","url":null,"abstract":"Clinical question classification is an important and a challenging task for any clinical Question Answering (QA) system. It classifies questions into different semantic categories, which indicate the expected semantic type of answers. Indeed, the semantic category allows filtering out irrelevant answer candidates. Existing methods dealing with the problem of clinical question classification don't take into account the syntactic dependency relations in questions. Therefore, this may impact negatively the performance of the clinical question classification system. To overcome this drawback, we propose to incorporate the syntactic dependency relations as discriminative features for machine learning. To evaluate and illustrate the interest of our contribution, we conduct a comparative study using nine methods and two machine-learning algorithms: Naive Bayes and Support Vector Machine (SVM). The obtained results using 4654 clinical questions maintained by the National Library of Medicine (NLM) show that our proposed method is very efficient and outperforms greatly the others by the average F-score of 4.5% for Naive Bayes and 4.73% for SVM.","PeriodicalId":434900,"journal":{"name":"Int. J. Bioinform. Res. Appl.","volume":"187 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115425809","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