The Transporter Classification Database (TCDB)

运输者分类数据库 (TCDB)

• 批准号: 7903633
• 负责人: MILTON H. SAIER
• 金额: $ 16.93万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-08-20 至 2010-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7903633
• 关键词: Adopted; Amino Acid Sequence; Anabolism; Binding; Binding Sites; Biochemical; Biochemistry; Biological Warfare; Biotechnology; Carbohydrates; Carrier Proteins; Cells; Cessation of life; Charge; Classification; Communication; Communities; Complex; Computer software; Coupling; Data; Data Analyses; Databases; Disease; Elements; Energy-Generating Resources; Enzymes; Eukaryota; Excretory function; Exons; Family; Generations; Genes; Genome; Goals; Hereditary Disease; Homologous Gene; Human Genetics; International; Introns; Ions; Kinetics; Lead; Life; Link; Lipids; Literature; Location; Mediating; Medicine; Membrane; Metabolism; Molecular Biology; Molecular Genetics; Multi-Drug Resistance; Nutrient; Operon; Organism; Paper; Peptide Sequence Determination; Pharmaceutical Preparations; Phylogenetic Analysis; Physiological; Process; Property; Protein Analysis; Protein Binding; Protein translocation; Proteins; Publications; Publishing; Reproduction; Research Personnel; Signaling Molecule; Software Design; Source; Specificity; Structure; System; Tertiary Protein Structure; Text; Tissues; Toxic effect; Toxin; Transport Process; Transport Protein Gene; Trees; Update; abstracting; base; design; fungus; gene terminator; hydropathy; information classification; inhibitor/antagonist; intercellular communication; macromolecule; member; neoplastic cell; novel; pathogenic bacteria; prevent; programs; promoter; repository; stoichiometry; tool; trimethylaminocarboxyldihydroboran; uptake

Transport systems provide essential functions for all living cells. Their importance to medicine cannot be overemphasized as (1) they provide a basis for multidrug resistance in pathogenic bacteria, fungi and protozoans as well as in tumor cells, (2) they are defective in numerous human genetic diseases, and (3) they are essential elements of toxin secretion systems by virtually all pathogenic organisms. We have developed a classification system for transport proteins called the Transporter Classification (TC) system. The TC system is a functional/phylogenetic system designed for the classification of all transmembrane transport proteins found in living organisms on Earth. It parallels but differs from the strictly functional EC system, developed decades ago by the Enzyme Commission of the International Union of Biochemistry and Molecular Biology (IUBMB) for the classification of enzymes. The TC system has recently been adopted by the IUBMB as the internationally acclaimed system to the classification of transporters. TCDB is a curated repository for factual information compiled from more than 10,000 references, encompassing approximately 3,000 representative transport proteins and putative transporters, classified into about 400 families. The primary goal of this proposal is to facilitate the updating, expansion and improvement of TCDB for use by the international scientific community. Our primary goals are first, to automate text classification and information extraction software so as to facilitate the continual updating of TCDB as newly published information about transporters becomes available (Specific Aims 1-3), and second, to devise software for the semiautomatic prediction of transport functions for putative transporters for which complete sequence data but little or no experimental data are available (Specific Aims 4-6). Our specific aims are to: (1) Incorporate into TCDB a text classification system for automatically identifying published literature describing newly characterized transport systems or previously characterized systems where new information is provided or old data are corrected. (2) Design information extraction software for incorporation of pertinent information from publications identified in specific aim #1 into TCDB. (3) Automate links to the primary literature from which the information in specific aim #2 was extracted as well as links to protein and operon analysis tools. (4) Incorporate software that will allow identification of motifs, signature sequences, protein domains, phylogenetic relationships and structural features for the proteins in TCDB and their homologues for the purpose of functional prediction. (5) Incorporate software that will facilitate the extraction of operon analysis data that can similarly be used for functional prediction. (6) Develop approaches that will allow integration of the different lines of functional information revealed in specific aims #4 and 5.

运输系统为所有活细胞提供基本功能。他们对医学的重要性不能 被过度强调为（1）它们为致病细菌，真菌和 原生动物以及在肿瘤细胞中，（2）它们在许多人类遗传疾病中有缺陷，（3） 它们是几乎所有病原生物的毒素分泌系统的重要元素。 我们已经开发了一种称为转运蛋白分类的传输蛋白的分类系统 （TC）系统。 TC系统是一个功能/系统发育系统，旨在分类 跨膜转运蛋白在地球上的生物体中发现。它相似，但与 严格的功能性EC系统，几十年前由国际酶委员会开发 生物化学和分子生物学联合（IUBMB），用于分类酶。 TC系统 IUBMB最近采用了国际知名的制度 运输商。 TCDB是​​一个精选的存储库，用于从10,000多个中汇编的事实信息 参考文献，包括大约3,000个代表性运输蛋白和推定转运蛋白， 分为大约400个家庭。该提案的主要目标是促进更新，扩展 以及TCDB的改进供国际科学界使用。 我们的主要目标是自动化文本分类和信息提取软件，以便自动化 随着有关转运者的新发布的信息，促进TCDB的持续更新 可用（特定目的1-3），其次是设计用于传输半自动预测的软件 完全序列数据但几乎没有实验数据的推定转运蛋白的功能是 可用（特定目标4-6）。 我们的具体目的是：（1）将自动的文本分类系统纳入TCDB 识别已发表的文献描述新特征的运输系统或以前 提供了提供新信息或更正旧数据的系统。 （2）设计信息 提取软件，用于从特定目的1中确定的出版物中合并相关信息 进入TCDB。 （3）自动链接指向主要文献的链接，特定目的＃2中的信息是 提取以及指向蛋白质和操纵子分析工具的链接。 （4）合并将允许的软件 鉴定基序，签名序列，蛋白质结构域，系统发育关系和结构 TCDB中蛋白质及其同源物的特征是为了进行功能预测的目的。 （5） 合并将有助于提取操纵子分析数据的软件，这些数据可以类似地用于 功能预测。 （6）开发将允许集成不同功能线的方法 特定目标＃4和5中揭示的信息。