Development of a comprehensive system for distant homology analysis

开发远距离同源性分析综合系统

• 批准号: 7943038
• 负责人: Adam Godzik
• 金额: $ 47.75万
• 依托单位: SANFORD BURNHAM PREBYS MEDICAL DISCOVERY INSTITUTE
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-30 至 2012-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7943038
• 关键词: Active Sites; Adopted; Algorithms; Amino Acid Sequence; Benchmarking; Binding; Code; Communication; Communities; Computer Systems Development; Data Quality; Databases; Development; Disease; Distant; Documentation; Evolution; Extensible Markup Language; Family; Frequencies; Goals; Grant; Human Genome; Imagery; Internet; Journals; Libraries; Licensing; Manuscripts; Metagenomics; Methods; Modeling; Modems; Molecular; Occupations; PAWR protein; Peer Review; Peptide Sequence Determination; Principal Investigator; Process; Protein Family; Proteins; Protocols documentation; Publications; Resources; Running; Sampling; Site; Source; Structure; System; Testing; Time; Training; Update; base; data exchange; design; flexibility; genome sequencing; graphical user interface; improved; meetings; multilevel analysis; open source; pathogen; programs; protein function; protein profiling; protein structure; protein structure function; protein structure prediction; research study; software systems; structural biology; structural genomics; tool; usability; user-friendly

In 2000, our Fold and Function Assignment System (FFAS) server pioneered protein profile-profile algorithms, applying them to protein structure prediction. Since then, the basic ideas underpinning these algorithms have been used in over 20 distant homology recognition algorithms, and the public FFAS server is used by almost 1,000 registered users running hundreds of jobs per day, applying the results not only in protein structure prediction, but also in function prediction, target selection in structural genomics, and general analysis of diverse protein families. With ever increasing flow of new protein sequence, many of them representing new, uncharacterized families, the importance of distant homology recognition is constantly growing. We propose enhancing the FFAS structure and interface to match these new types of applications, developing the server into a major resource for studying broad and diversified protein families. We plan to extend the usefulness and maintainability of FFAS by restructuring its code using modem programming practices to develop a modular, multistage program ready to be integrated with other servers, as well as use other programs, developed both inside and outside our group, to improve quality of data at each step of the prediction process and also to export intermediate results to the user for analysis. By extending the set of analysis and visualization tools integrated into the FFAS server and improving its user interface, we want to make it easier to be used by a generally trained biologist. Finally, we plan to perform a significant hardware update to avoid delays in providing annotations for user-submitted sequences.

2000年，我们的折叠和功能分配系统(FFAs)服务器率先推出了蛋白质 Profile-Profile算法，将其应用于蛋白质结构预测。从那以后， 支撑这些算法的基本思想已经在20多个遥远的地方被使用 同源识别算法，并且公共的FFAs服务器几乎被使用 1,000个注册用户每天运行数百个作业，将结果应用于 不仅在蛋白质结构预测方面，而且在功能预测、靶点选择方面也是如此 结构基因组学，以及对不同蛋白质家族的一般分析。永远不变 不断增加的新蛋白质序列，其中许多代表新的， ，远距离同源识别的重要性是 不断增长。我们建议加强FFA的结构和接口，以 匹配这些新类型的应用程序，将服务器开发为主要资源 用于研究广泛和多样化的蛋白质家族。我们计划扩大它的用途 并通过使用现代编程重新编写其代码来实现FFA的可维护性 开发模块化、多阶段计划的实践，以便与其他计划集成 服务器，以及使用我们内部和外部开发的其他程序 以提高预测过程每个步骤的数据质量，并 将中间结果导出给用户进行分析。通过扩展分析集合 和可视化工具集成到FFAS服务器中并改进其用户 界面，我们想让它更容易被一般训练有素的生物学家使用。 最后，我们计划执行一次重要的硬件更新，以避免延迟提供 用户提交的序列的注释。