The Transporter Classification Database (TCDB)

运输者分类数据库 (TCDB)

• 批准号: 9895808
• 负责人: MILTON H. SAIER
• 金额: $ 31.5万
• 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 2022-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9895808
• 关键词: Activator Appliances; Adopted; Affect; Alternative Splicing; Antimicrobial Resistance; Antineoplastic Agents; Biochemical; Biochemistry; Biological Phenomena; Biology; Biotechnology; Carrier Proteins; Cells; Chemicals; Classification; Collaborations; Communities; Complement; Computer software; Data; Database Management Systems; Databases; Development; Ecosystem; Ensure; Eukaryota; Family; Funding; Genetic Diseases; Genome; Genomics; Goals; Grant; Health; Homeostasis; Human Genetics; Individual; Information Resources; International; Investigation; Island; Knowledge; Laboratories; Life; Ligands; Literature; Machine Learning; Medical; Medicine; Membrane Proteins; Metabolic; Metabolism; Methods; Modeling; Modernization; Molecular; Molecular Biology; Multi-Drug Resistance; Ontology; Organelles; Pathogenesis; Pathologic; Pharmaceutical Preparations; Phenotype; Physiological; Play; Post-Translational Protein Processing; Production; Protein Isoforms; Proteins; Pump; RNA Splicing; Research; Research Personnel; Role; Scientist; Stimulus; Structure; System; Systems Biology; Tertiary Protein Structure; Time; Tissues; Training; Transmembrane Transport; Update; Variant; Vertebral column; Work; Xenobiotics; base; data pipeline; drug development; improved; inhibitor/antagonist; insight; member; metagenome; novel; pathogen; personalized medicine; protein transport; screening; text searching; transmission process; tumor; whole genome; willingness

ABSTRACT 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 evolutionary 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 system and constituent proteins. It also includes a superfamily hyperlink. In this competitive renewal of GM0077402, we propose to continue to expand, update, and semi-automate TCDB. Our specific aims are to (1) upgrade TCDB by characterizing and categorizing protein domains and their topologies, motifs, repeat units, functional interactions, alternative splicing and post-translational modifications, (2) expand TCDB by implementing novel pipelines for data entry that will increase the coverage of transport diversity in TCDB while describing more effectively the complexity of multicomponent transport systems, (3) enter into TCDB transporter modulators such as activators, inhibitors, drugs and xenobiotics as well as internal and external conditions that influence transporter activities, while generating an ontology to describe the effects of chemical modulators that will complement our substrate ontology, (4) incorporate into TCDB synthetic pores/channels (TC subclass 1.D), and carriers (TC subclass 2.B), (5) introduce into TCDB connections between transport and metabolism and (6) expand our plans for long-term TCDB sustainability.

抽象的 转运蛋白催化分子进入和流入细胞和细胞器。他们 达到细胞稳态，负责病原体和肿瘤中的多药耐药性，以及 当缺陷时，引起数十种重要的人遗传疾病。我们的实验室维护，更新 并改善运输者分类数据库TCDB，该数据库容纳运输蛋白 分类（TC）系统，由国际生物化学和分子联盟正式通过 生物学（IUBMB）。 TCDB是​​国际知名，精心注释的通用标准 在所有主要专业中分类和提供有关转运蛋白和运输相关蛋白的信息 生活领域。它介绍了序列，生化，生理，病理，结构和 有关这些蛋白质及其构成的传输系统的进化数据。它使用了成功 基于运输者类，子类，家庭，亚家族，个人运输的分类系统 系统和组成蛋白。它还包括超级家庭超链接。 在GM0077402的这种竞争续约中，我们建议继续扩展，更新和 半自动TCDB。我们的具体目的是（1）通过表征和分类来升级TCDB 蛋白质域及其拓扑，基序，重复单元，功能相互作用，替代剪接 （2）通过实施数据输入的新型管道来扩展TCDB（2）扩展TCDB 这将增加TCDB运输多样性的覆盖范围，同时更有效地描述 多组分传输系统的复杂性，（3）输入TCDB转运器调制器，例如 激活剂，抑制剂，药物和异种生物以及影响的内部和外部条件 转运蛋白活动，同时产生本体来描述化学调节剂的影响 将补充我们的底物本体论，（4）纳入TCDB合成孔/通道（TC） 子类1.D）和载体（TC子类2.b），（5）引入运输之间的TCDB连接 以及新陈代谢以及（6）扩大我们长期TCDB可持续性的计划。