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1.
糖基化修饰是生物体内最常见、最重要的蛋白质翻译后修饰之一.哺乳动物体内超过50%的蛋白质都会发生糖基化修饰.糖蛋白广泛分布于各种组织的细胞膜表面,执行着重要的生物学功能.随着高通量、高灵敏度和高分辨率的蛋白质组学时代的来临,许多基于串级质谱技术解析糖链结构的生物数据库和分析软件也亦应运而生.本文综述了目前文献中最常用的糖类生物信息学资源,包括各种糖蛋白的数据库以及质谱解析糖类的相关工具和新技术、新方法.  相似文献   

2.
糖生物信息学是在糖生物学和糖组学发展的基础上,结合计算机技术,对生命活动过程中,参与糖链及与其相互作用的蛋白质等分子研究所产生的数据进行获取、储存、解析、模拟以及预测等内容的综合学科.糖生物信息学数据库是糖生物信息学发展到一定阶段,对糖组学等研究中产生的数据进行专门储藏与查询的应用工具.目前国际互联网中存在近百个糖生物信息学相关数据库,涉及内容包括糖链结构、参与糖链合成的基因或者蛋白质、糖结合蛋白、代谢通路、糖链或相互作用蛋白质等分子三维结构,或糖组学实验结果等领域.本文将归纳总结糖生物信息学数据库,为现有研究提供帮助.  相似文献   

3.
糖、糖、“糖”——什么是糖?   总被引:1,自引:0,他引:1  
糖类是自然界中最常见的一类生物分子,但是糖类因不同的人群可以有三种不同的理解.一是科学上的糖类,二是生活中的糖类,三是作为甜味剂的"糖"类.因为甜味是一个生理上的感觉,凡能与甜味受体相互作用的均是甜味剂,其中有些是糖的"糖",也有不是糖的"糖".  相似文献   

4.
利用SWISS-PROT网上获取生物信息学资源   总被引:3,自引:0,他引:3  
生物信息学是是采用数学、统计学和计算机方法对生物学数据信息进行采集、存储、传播、分析、归类、解释的科学[1].Internet网络是信息传输、检索、获取、交流的重要手段.当前,在Internet网上可以查询到大量的生物信息学数据库,其中SWISS-PROT蛋白质序列数据库是网上生物信息学最核心的3个数据库之一.通过该数据库,可以较完整地获得生物大分子的序列信息.同时,研究者也可以将测定的序列信息通过该数据库予以认定、发表、交流.本文主要探讨SWISS-PROT蛋白质序列数据库的特点、检索方法及利用Internet获取蛋白质序列信息.  相似文献   

5.
生物信息学策略鉴定新基因   总被引:1,自引:0,他引:1  
随着人类基因组计划的开展,在基因结构、定位、表达和功能研究等方面都积累了大量的数据,如何充分利用大量已有的网上数据库资源,加速人类基因克隆研究及功能初步研究,同时避免重复工作,节省开支,已成为我们面临的一个急迫而富有挑战性的课题.生物信息学是20世纪80年代末开始,随着基因组测序数据迅猛增加而逐渐兴起的一门新兴学科,它利用计算机对生命科学研究中的生物信息进行存储、检索和分析.它的产生和发展为人们提供了强大的工具,本文就生物信息学方法在识别和鉴定新基因中的应用予以综述.  相似文献   

6.
纳米材料在电子学、光学、磁学和生物医药等方面有着广泛的应用。在过去的20年,金属纳米微粒已经成功地与多肽、蛋白质和DNA结合,但糖类物质直到2001年才被引入到纳米科学中。糖纳米微粒能够很好地构建类似细胞表面糖类表达的生物细胞模型,成为糖生物学、生物药学、材料科学中十分出色的研究工具。随着研究的深入,糖纳米材料由于其制备简便,具有独特的物理、化学和生物性质,其在生物医学成像、诊断及治疗等方面有着广泛的应用前景。  相似文献   

7.
功能糖的抗肿瘤和防治肝病作用   总被引:1,自引:0,他引:1  
糖类药物研究是基于糖生物学取得的重要进展,以生命体内糖链信息分子的结构、功能为依据,基于细胞粘附和细胞表面糖链识别为靶标的研究。主要研究方向是:新的寡糖化学合成的方法和策略:重要生物活性寡糖的合成及其活性评价;糖苷酶、糖基转移酶抑制剂的设计、合成、评价,以及对天然产物中分离得到的糖类药物进行鉴定和评价。而今已有一些功能糖作为糖类药物在抗肿瘤和防治肝病中得到了一定的应用,并且这种应用正在被人们逐步认知和接受。  相似文献   

8.
基于生物信息学方法发现潜在药物靶标   总被引:2,自引:0,他引:2       下载免费PDF全文
药物靶点通常是在代谢或信号通路中与特定疾病或病理状态有关的关键分子.通过绑定到特定活动区域抑制这个关键分子进行药物设计.确定特定疾病有关的靶标分子是现代新药开发的基础.在药物靶标发现的过程中,生物信息学方法发挥了不可替代的重要的作用,尤其适用于大规模多组学数据的分析.目前,已涌现了许多与疾病相关的数据库资源,基于生物网络特征、多基因芯片、蛋白质组、代谢组数据等建立了多种生物信息学方法发现潜在的药物靶标,并预测靶标可药性和药物副作用.  相似文献   

9.
生物信息学的发展产生了越来越多的数据库和生物学软件,研究人员在应用这些生物学工具处理实验数据时需要大量的时间解决数据格式转换和管理等问题。本文介绍了一种交互式的基于网络的新一代生物信息学分析平台一Swam,它综合了主要的生物信息学数据库和软件,可以加速数据处理并帮助用户管理数据。因此它将推动生物信息学向更深层次发展。  相似文献   

10.
糖是生物体内主要的碳源,是光合作用的主要产物,可为生物体提供能量,在植物的生长发育过程中起重要作用。本文综述了近年来关于糖类与果树生长发育及品质形成方面的相关研究进展,重点介绍了糖类运输、积累与基因表达、糖信号传导和糖类调控网络等方面的研究进展,并对今后利用分子生物学手段进行果实品质改良等方面的研究方向进行了展望。  相似文献   

11.
Bioinformatics has played a pivotal role in advancing genetics and protein sciences. The large amount of information generated by genomics, and now proteomics, has been a driving force. By comparison, glycobiology still generates small amounts of data. The need to organize our knowledge about carbohydrates is however growing constantly and has given rise to an increasing number of public databases and freely available tools. This review gives an overview of the carbohydrate-oriented resources currently available on the Internet. Many of the resources are seldom referred to in the literature and difficult to find, in part because of the constant flux of the net itself, but also because many efforts have been lead by a single individual. As the World Wide Web has matured the number of 'permanent' resources, maintained by organizations rather than individuals, has increased. In this paper, we present some of the more useful and accessible public tools and databases. There are also a few commercial initiatives but these have not been reviewed.  相似文献   

12.
Researchers are increasingly depending on various centralized resources to access the vast amount of information reported in the literature and generated by systematic sequencing and functional genomics projects. Biological databases have become everyday working tools for many researchers. This dependency goes both ways in that the databases require continuous feedback from the research community to maintain accurate, reliable, and upto- date information. The fission yeast Schizosaccharomyces pombe has recently been sequenced, setting the stage for the post-genome era of this popular model organism. Here, we provide an overview of relevant databases available, or being developed, together with a compilation of Internet resources containing useful information and tools for fission yeast.  相似文献   

13.
Hong CB  Kim YJ  Moon S  Shin YA  Cho YS  Lee JY 《BMB reports》2012,45(1):47-50
The International HapMap Project and the Human Genome Diversity Project (HGDP) provide plentiful resources on human genome information to the public. However, this kind of information is limited because of the small sample size in both databases. A Genome-Wide Association Study has been conducted with 8,842 Korean subjects as a part of the Korea Association Resource (KARE) project. In an effort to build a publicly available browsing system for genome data resulted from large scale KARE GWAS, we developed the KARE browser. This browser provides users with a large amount of single nucleotide polymorphisms (SNPs) information comprising 1.5 million SNPs from population-based cohorts of 8,842 samples. KAREBrowser was based on the generic genome browser (GBrowse), a webbased application tool developed for users to navigate and visualize the genomic features and annotations in an interactive manner. All SNP information and related functions are available at the web site http://ksnp.cdc. go.kr/karebrowser/.  相似文献   

14.
The field of proteomics is advancing rapidly as a result of powerful new technologies and proteomics experiments yield a vast and increasing amount of information. Data regarding protein occurrence, abundance, identity, sequence, structure, properties, and interactions need to be stored. Currently, a common standard has not yet been established and open access to results is needed for further development of robust analysis algorithms. Databases for proteomics will evolve from pure storage into knowledge resources, providing a repository for information (meta-data) which is mainly not stored in simple flat files. This review will shed light on recent steps towards the generation of a common standard in proteomics data storage and integration, but is not meant to be a comprehensive overview of all available databases and tools in the proteomics community.  相似文献   

15.
The development of efficient DNA sequencing methods has led to the achievement of the DNA sequence of entire genomes from (to date) 55 prokaryotes, 5 eukaryotic organisms and 10 eukaryotic chromosomes. Thus, an enormous amount of DNA sequence data is available and even more will be forthcoming in the near future. Analysis of this overwhelming amount of data requires bioinformatic tools in order to identify genes that encode functional proteins or RNA. This is an important task, considering that even in the well-studied Escherichia coli more than 30% of the identified open reading frames are hypothetical genes. Future challenges of genome sequence analysis will include the understanding of gene regulation and metabolic pathway reconstruction including DNA chip technology, which holds tremendous potential for biomedicine and the biotechnological production of valuable compounds. The overwhelming volume of information often confuses scientists. This review intends to provide a guide to choosing the most efficient way to analyze a new sequence or to collect information on a gene or protein of interest by applying current publicly available databases and Web services. Recently developed tools that allow functional assignment of genes, mainly based on sequence similarity of the deduced amino acid sequence, using the currently available and increasing biological databases will be discussed.  相似文献   

16.
TreeGenes and tree fruit Genome Database Resources serve the international forestry and fruit tree genomics research communities, respectively. These databases hold similar sequence data and provide resources for the submission and recovery of this information in order to enable comparative genomics research. Large-scale genotype and phenotype projects have recently spawned the development of independent tools and interfaces within these repositories to deliver information to both geneticists and breeders. The increase in next generation sequencing projects has increased the amount of data as well as the scale of analysis that can be performed. These two repositories are now working towards a similar goal of archiving the diverse, independent data sets generated from genotype/phenotype experiments. This is achieved through focused development on data input standards (templates), pipelines for the storage and automated curation, and consistent annotation efforts through the application of widely accepted ontologies to improve the extraction and exchange of the data for comparative analysis. Efforts towards standardization are not limited to genotype/phenotype experiments but are also being applied to other data types to improve gene prediction and annotation for de novo sequencing projects. The resources developed towards these goals represent the first large-scale coordinated effort in plant databases to add informatics value to diverse genotype/phenotype experiments.  相似文献   

17.
To have a better understanding of the mechanisms of disease development, knowledge of mutations and the genes on which the mutations occur is of crucial importance. Information on disease-related mutations can be accessed through public databases or biomedical literature sources. However, information retrieval from such resources can be problematic because of two reasons: manually created databases are usually incomplete and not up to date, and reading through a vast amount of publicly available biomedical documents is very time-consuming. In this paper, we describe an automated system, MuGeX (Mutation Gene eXtractor), that automatically extracts mutation-gene pairs from Medline abstracts for a disease query. Our system is tested on a corpus that consists of 231 Medline abstracts. While recall for mutation detection alone is 85.9%, precision is 95.9%. For extraction of mutation-gene pairs, we focus on Alzheimer's disease. The recall for mutation-gene pair identification is estimated at 91.3%, and precision is estimated at 88.9%. With automatic extraction techniques, MuGeX overcomes the problems of information retrieval from public resources and reduces the time required to access relevant information, while preserving the accuracy of retrieved information.  相似文献   

18.
The rapidly increasing amount of information on three-dimensional (3D) structures of biological macro-molecules has still an insufficient impact on genome analysis, functional genomics and proteomics as well as on many other fields in biomedicine including disease-related research. There are, however, attempts to make structural data more easily accessible to the bench biologist. As members of the world-wide Protein Data Bank (wwPDB), the RCSB Protein Data Bank (PDB), the Protein Data Bank Japan and the Macromolecular Structure Database are the primary information resources for 3D structures of proteins, nucleic acids, carbohydrates and complexes thereof. In addition, a number of secondary resources have been set up that also provide information on all currently known structures in a relatively comprehensive manner and not focusing on specific features only. They include PDBsum, the OCA browser-database for protein structure/function, the Molecular Modeling Database and the Jena Library of Biological Macromolecules--JenaLib. Both the primary and secondary resources often merge the information in the PDB files with data from other resources and offer additional analysis tools thereby adding value to the original PDB data. Here, we briefly describe these resources from a user's point of view and from a comparative perspective. It is our aim to guide researchers outside the structure biology field in getting the most out of the 3D structure resources.  相似文献   

19.
20.
Acclimation of photosynthesis to light: a mechanistic approach   总被引:9,自引:0,他引:9  
  相似文献   

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