2010 IEEE International Conference on BioInformatics and BioEngineering最新文献_第5页

Knowledge-Guided Docking of Flexible Ligands to SH2 Domain Proteins 知识引导下柔性配体与SH2结构域蛋白的对接

2010 IEEE International Conference on BioInformatics and BioEngineering Pub Date : 2010-05-31 DOI: 10.1109/BIBE.2010.37

Haiyun Lu, Shamima Rashid, Hao Li, W. Leow, Y. Liou

{"title":"Knowledge-Guided Docking of Flexible Ligands to SH2 Domain Proteins","authors":"Haiyun Lu, Shamima Rashid, Hao Li, W. Leow, Y. Liou","doi":"10.1109/BIBE.2010.37","DOIUrl":"https://doi.org/10.1109/BIBE.2010.37","url":null,"abstract":"Studies of interactions between protein domains and ligands are important in many aspects such as cellular signaling and regulation. In this work, we applied a three-stage knowledge-guided approach of docking flexible peptide ligands to SH2 domains. The first stage of the approach search for binding pockets of SH2 domain proteins and binding motifs of peptide ligands based on known features. The knowledge of the binding sites are used in the second stage as binding constraints to align ligand's peptide backbone to the SH2 domain. The backbone-aligned ligands produced serve as good starting points to the third stage which uses a Monte Carlo method to perform the flexible docking. The experimental results show that the backbone alignment method at the second stage produces good backbone conformations which are close to the conformation in complex. The binding site information is well utilized to provide a better starting point to the next docking stage. The subsequent docking is successful or partially successful in 5 of 7 test cases. The performance is better than that of general docking methods. The presented approach can also be applied to other well characterized protein domains which bind ligands in two or more binding grooves.","PeriodicalId":330904,"journal":{"name":"2010 IEEE International Conference on BioInformatics and BioEngineering","volume":"48 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130907468","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

Instance Discovery and Schema Matching with Applications to Biological Deep Web Data Integration 实例发现与模式匹配在生物深度网络数据集成中的应用

2010 IEEE International Conference on BioInformatics and BioEngineering Pub Date : 2010-05-31 DOI: 10.1007/978-3-642-15120-0_12

Tantan Liu, Fan Wang, G. Agrawal

引用次数: 4

A Self-Healing Approach for a Domain-Specific Deep Web Search Tool 特定领域深度网络搜索工具的自修复方法

2010 IEEE International Conference on BioInformatics and BioEngineering Pub Date : 2010-05-31 DOI: 10.1109/BIBE.2010.13

Fan Wang, G. Agrawal

引用次数: 1

Ethanol Effects on Transcription Factor Network Regulating Stem Cell Differentiation 乙醇对调控干细胞分化的转录因子网络的影响

2010 IEEE International Conference on BioInformatics and BioEngineering Pub Date : 2010-05-31 DOI: 10.1109/BIBE.2010.62

R. Vadigepalli, Joshua Ogony, H. Anni

{"title":"Ethanol Effects on Transcription Factor Network Regulating Stem Cell Differentiation","authors":"R. Vadigepalli, Joshua Ogony, H. Anni","doi":"10.1109/BIBE.2010.62","DOIUrl":"https://doi.org/10.1109/BIBE.2010.62","url":null,"abstract":"This study probes the effects of ethanol on the molecular mechanisms regulating the differentiation of embryonic stem (ES) cells towards neuroectodermal state, which may be responsible for the abnormalities observed in fetal alcohol spectrum disorders (FASD). The effects of ethanol on the early phase of ES cell differentiation have not been well characterized. Here, we investigate the stage-specific action of ethanol during early embryogenesis by an integrated experimental and computational modeling approach. Our experimental system consists of mouse ES cells and directed differentiation to neuroectodermal fate in the presence of ethanol. Experimental single-cell multiplex data on the expression of the ES core transcription factors (TFs), Sox2, Oct4 and Nanog were obtained simultaneously by multicolor flow cytometry in live cells. Singlecell flow cytometric data were analyzed by ARACNE probabilistic modeling to construct transcriptional regulatory networks and quantify the TFs interactions in a pairwisemanner. Our analysis indicates that during differentiation towards neuroectodermal fate ethanol accelerates (i) the decline of the expression levels of Sox2 and Nanog, and (ii) the decreasing strength of the correlative interactions between the core TFs which is also reflected in (iii) an advanced differentiation phenotype.","PeriodicalId":330904,"journal":{"name":"2010 IEEE International Conference on BioInformatics and BioEngineering","volume":"12 1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123665500","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

Modular Software Design for Brachytherapy Image-Guided Robotic Systems 近距离影像引导机器人系统的模块化软件设计

2010 IEEE International Conference on BioInformatics and BioEngineering Pub Date : 2010-05-31 DOI: 10.1109/BIBE.2010.40

Ivan Buzurovic, T. Podder, L. Fu, Yan Yu

引用次数: 6

A Multi-stage Spectral Alignment Strategy for Unrestrictive PTM Peptide Identification 无限制性PTM多肽鉴定的多阶段光谱比对策略

2010 IEEE International Conference on BioInformatics and BioEngineering Pub Date : 2010-05-31 DOI: 10.1109/BIBE.2010.11

Changyong Yu, Guoren Wang, Yuhai Zhao, Keming Mao

{"title":"A Multi-stage Spectral Alignment Strategy for Unrestrictive PTM Peptide Identification","authors":"Changyong Yu, Guoren Wang, Yuhai Zhao, Keming Mao","doi":"10.1109/BIBE.2010.11","DOIUrl":"https://doi.org/10.1109/BIBE.2010.11","url":null,"abstract":"Spectral alignment, which studies the matching of ion peaks between the investigated spectrum and theoretical spectrum of peptide in the peptide database, is a very useful topic in computational proteomics. So far, the efficient, accurate and practical spectral alignment algorithm is still urgently needed due to its important application in the PTM unrestrictive peptide identification. In this paper, a multi-stage spectral alignment algorithm called MS-SA is proposed with the following two features: (a) it provided four different levels of alignment aims according to the alignment quality which can be specified by users, (b) it provided the capability of analyzing the detail modification types and locations for spectrum with multiple PTM sites. Therefore, MS-SA is of high practicality and can be applied to different specific applications such as being a filter in the large-scale database searching, a tool for detail modification types and locations analysis in small-scale spectral alignment and so on. A large number of experiments on real MS/MS data have been done for testing the performance of MS-SA. Also, the results of MS-SA are compared with those of same type of algorithms such as SA and SPC. The results show that MS-SA possesses strong practicality and outperforms the SA and SPC algorithms on several aspects.","PeriodicalId":330904,"journal":{"name":"2010 IEEE International Conference on BioInformatics and BioEngineering","volume":"20 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131740735","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

Learning Proteomic Network Structure by a New Hill Climbing Algorithm 一种新的爬坡算法学习蛋白质组网络结构

2010 IEEE International Conference on BioInformatics and BioEngineering Pub Date : 2010-05-31 DOI: 10.1109/BIBE.2010.38

Dongchul Kim, Jean X. Gao, Chin-Rang Yang

引用次数: 0

Detection of Mild Cognitive Impairment Using Image Differences and Clinical Features 利用图像差异和临床特征检测轻度认知障碍

2010 IEEE International Conference on BioInformatics and BioEngineering Pub Date : 2010-05-31 DOI: 10.1109/BIBE.2010.26

Lin Li, J. Wang, Dheeraj Chahal, M. Eckert, Carl Lozar

{"title":"Detection of Mild Cognitive Impairment Using Image Differences and Clinical Features","authors":"Lin Li, J. Wang, Dheeraj Chahal, M. Eckert, Carl Lozar","doi":"10.1109/BIBE.2010.26","DOIUrl":"https://doi.org/10.1109/BIBE.2010.26","url":null,"abstract":"In this study, we present a systematic method for early detection of mild cognitive impairment (MCI) from magnetic resonance images (MRI) using image differences and clinical features. Early detection of MCI has pivotal importance to delay or prevent the onset of Alzheimer’s disease (AD). Subjects were selected from the Open Access Series of Imaging Studies (OASIS)database and included 89 MCI subjects and 80 controls. T1 weighted MRI scans were analyzed to identify their voxel-by-voxel differences in gray matter (GM) intensity between MCI group and control group. Based on the differences, a threshold-based unseeded region growing algorithm was designed to determine multiple regions which atrophy is characteristic of MCI. A feature ranking method was then adopted to select a small number of regions that presented relatively more pronounced atrophy. Next, support vector machine (SVM) based classification was applied by using the clinical features of subjects and the features of selected regions. Our method was tested by leave-one-out cross-validation and it demonstrated high classification accuracy (90%).","PeriodicalId":330904,"journal":{"name":"2010 IEEE International Conference on BioInformatics and BioEngineering","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114182918","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: 3

Combining Prostate Cancer Region Predictions from MALDI Spectra Processing and Texture Analysis 结合MALDI光谱处理和纹理分析的前列腺癌区域预测

2010 IEEE International Conference on BioInformatics and BioEngineering Pub Date : 2010-05-31 DOI: 10.1109/BIBE.2010.20

Jiang Li, A. Vadlamudi, Shao-Hui Chuang, Xiaoyan Sun, Bo Sun, F. McKenzie, L. Cazares, J. Nyalwidhe, D. Troyer, O. Semmes

引用次数: 2

Assessment of the Binding Characteristics of Human Immunodeficiency Virus Type 1 Glycoprotein120 and Host Cluster of Differentiation4 Using Digital Signal Processing 利用数字信号处理评估人类免疫缺陷病毒1型糖蛋白120与宿主分化簇4的结合特性

2010 IEEE International Conference on BioInformatics and BioEngineering Pub Date : 2010-05-31 DOI: 10.1109/BIBE.2010.57

N. Nwankwo, H. Seker

{"title":"Assessment of the Binding Characteristics of Human Immunodeficiency Virus Type 1 Glycoprotein120 and Host Cluster of Differentiation4 Using Digital Signal Processing","authors":"N. Nwankwo, H. Seker","doi":"10.1109/BIBE.2010.57","DOIUrl":"https://doi.org/10.1109/BIBE.2010.57","url":null,"abstract":"Protein residues which contribute to bio-recognition and binding interaction between HIV Surface protein also called Glycoprotein120 (gp120) and Cluster of Differentiation4 (CD4) have been identified. However, this was with limited number of isolates. Notwithstanding, the particular HIV isolate that harbors the gp120 with the greatest binding force to the CD4 has not been investigated. In this paper, protein sequences of gp120 from 43 HIV-1 isolates, 5 isolates each from the HIV-2 and SIV as well as the CD4 of 25 HIV host organisms were analyzed using Resonant Recognition Method (RMM). The results re-confirmed that protein sequences of the HIV and CD4 share common spectral features in relation to bio-recognition and binding. From the large dataset of the HIV and SIV isolates used, MFA group M subtype B (HIV-1) isolate was found to have the greatest affinity for the CD4. Furthermore, the CD4 of the human and chimpanzee were established to possess about same level of binding force to the HIV gp120. Also the CD4 of other species offered more attractive force to another protein in such a manner that the approach taken in this study has also shown to be a useful and reliable tool for clear categorization of species. Finally, clinically experimented results were found to correlate with the computationally obtained results as the gp120 of the HIV-2 and SIV which were recognized to circumvent the CD4 during infection were found to have low peak amplitude. This low peak amplitude observed in the HIV-2 and SIV implies that they have weak affinity or attraction for the host CD4.","PeriodicalId":330904,"journal":{"name":"2010 IEEE International Conference on BioInformatics and BioEngineering","volume":"15 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114081860","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