The Transporter Classification Database (TCDB)

运输者分类数据库 (TCDB)

• 批准号: 9011535
• 负责人: MILTON H. SAIER
• 金额: $ 30.23万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-04-01 至 2019-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9011535
• 关键词: Address; Adopted; Binding Proteins; Binding Sites; Biochemical; Biochemistry; Biological; Biological Process; Biology; Carrier Proteins; Cells; Chemicals; Cistrons; Classification; Collaborations; Communities; Computer software; Controlled Vocabulary; Data; Data Base Management; Databases; Detection; Development; Distant; Ecosystem; Family; Funding; Goals; Hereditary Disease; Homeostasis; Homologous Gene; Housing; Human Genetics; Individual; Information Resources; International; Internet; Island; Knowledge; Laboratories; Language; Lead; Life; Maintenance; Methodology; Methods; Modernization; Molecular Biology; Multi-Drug Resistance; Ontology; Operon; Organelles; Pattern; Pharmaceutical Preparations; Phylogenetic Analysis; Phylogeny; Physiological; Printing; Procedures; Protein Family; Proteins; Protocols documentation; Publishing; Recurrence; Regulon; Research Personnel; Scientist; Seeds; Signal Transduction; Source; Statistical Methods; Structure; Synteny; System; Technology; Tertiary Protein Structure; Testing; Time; Toxin; Training; Transmembrane Transport; Update; base; computer science; design; genome annotation; improved; inhibitor/antagonist; innovation; insight; knowledge base; markov model; novel; novel strategies; pathogen; programs; protein transport; public health relevance; text searching; transcriptome; transmission process; tumor; whole genome

DESCRIPTION (provided by applicant): Transporters catalyze entry and exit of molecules into and out of cells and organelles. They achieve cellular homeostasis, are responsible for multidrug resistance in pathogens and tumors, and when defective, cause dozens of important human genetic diseases. Our laboratory maintains, updates and improves the Transporter Classification Database, TCDB, which houses the Transporter Classification (TC) system, adopted officially by the International Union of Biochemistry and Molecular Biology (IUBMB). TCDB is the internationally acclaimed, carefully annotated, universal standard for classifying and providing information about transporters and transport-related proteins in all major domains of life. It presents sequence, biochemical, physiological, pathological, structural and evolutionar data about these proteins and the transport systems they comprise. It uses a successful system of classification based on transporter class, subclass, family, subfamily, individual transport systems and constituent proteins. In this competitive renewal of GM0077402, we propose to expand, update, automate and interlink TCDB. In particular, we will collaborate to integrate and unify the classification systems used by TCDB and Pfam with the formation of a TC ontological system. We will generate new data concerning transport proteins, and expand procedures for making functional predictions. This last effort will derive reliable new biological knowledge from a variety of sources, including phylogeny, motif, domain, operon and regulon analyses. Our Specific Aims are as follows: 1. To compare and evaluate methods of homology establishment, e.g., our and Pfam's statistical approaches, as well as introduce a system of protein repeat unit and domain identification. We will confirm and extend homology results based on structural superimpositions and profile: profile comparisons. We will develop and implement pipelines for the exchange of information between Pfam and TCDB and standardize both classification systems. 2. To incorporate our family descriptions into Wikipedia, to facilitate community annotation and interaction. Thus, we will add to Wikipedia, and integrate with Pfam to create a common platform for community annotation. 3. To create a substrate ontological framework for TCDB, using ChEBI and GO. 4. To use and automate multiple approaches, including phylogeny and synteny, to derive reliable functional predictions and provide guides for other researchers to do the same. 5. To utilize our TCDB advisory board for continued knowledgebase modernization and sustainability.

描述（由申请人提供）：转运蛋白催化分子进入和流入细胞和细胞器。它们实现了细胞稳态，负责病原体和肿瘤中的多药耐药性，并且在缺陷时会导致数十种重要的人类遗传疾病。我们的实验室维护，更新和改进了运输者分类数据库TCDB，该数据库包含运输者分类（TC）系统，该系统由国际生物化学和分子生物学联盟（IUBMB）正式通过。 TCDB是​​国际知名的，精心注释的通用标准，用于分类和提供有关运输者和运输相关蛋白质的信息。它介绍了有关这些蛋白质及其构成的传输系统的序列，生化，生理，病理，结构和进化数据。它使用基于运输者类，子类，家庭，亚家族，单个运输系统和组成蛋白的成功分类系统。 在GM0077402的这种竞争续约中，我们建议扩展，更新，自动化和互联链接TCDB。特别是，我们将合作地集成和统一TCDB和PFAM使用的分类系统与TC本体论系统的形成。我们将生成有关运输蛋白的新数据，并扩展进行功能预测的程序。最后的努力将从多种来源获得可靠的新生物学知识，包括系统发育，基序，域，操纵子和调节分析。我们的具体目的如下：1。要比较和评估同源性建立的方法，例如我们和PFAM的统计方法，并引入了蛋白质重复单元和域识别系统。我们将基于结构叠加和概况：轮廓比较确认并扩展同源结果。我们将开发和实施管道来交换PFAM和TCDB之间的信息，并标准化两个分类系统。 2。将我们的家庭描述纳入Wikipedia，以促进社区注释和互动。因此，我们将添加到Wikipedia中，并与PFAM集成以创建一个共同的社区注释平台。 3。要使用Chebi和Go为TCDB创建一个底物本体论框架。 4。使用和自动化多种方法，包括系统发育和同步，以得出可靠的功能预测，并为其他研究人员提供同样的指南。 5。利用我们的TCDB顾问委员会进行持续的知识库现代化和可持续性。