New Algorithms for Detecting Sequence and Structure Similarities

检测序列和结构相似性的新算法

• 批准号: 7594480
• 负责人: Teresa M. Przytycka
• 金额: $ 15.89万
• 依托单位: NATIONAL LIBRARY OF MEDICINE
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/7594480
• 关键词: Algorithms; Amino Acid Sequence; Arts; Attention; Base Sequence; Complement; Databases; Detection; Development; Evolution; Goals; Hand; Manuals; Methods; Modeling; Peptide Sequence Determination; Protein Family; Proteins; Sequence Alignment; Structure; Work; base; indexing; interest; novel strategies; protein function; protein structure prediction; tool

The project is divided into 4 subprojects: 1.Iterative automatic methods for refining multiple sequence alignment. Currently starting point of constructing CDD database is a multiple alignment imported form protein family models as SMART and PFAM. Since all known multiple sequence alignment algorithms are less than perfect the imported alignment have errors that are now removed by hand. The goal of the project is to provide reduce and simplify this manual work (ref. 1). 2.New approaches for detecting structural similarities. The goal of this subproject is to develop new approaches for fast detection of structural similarities that would complement currently used method (VAST). Thus particular attention is given to loop structure and developing of indexing methods (ref 7). 3.Applications of methods based on sequence and structure similarities to study protein evolution (and co-evolution). Particular interests include prediction of protein interaction from sequence co-evolution (ref 3,4,6). 4. Classifaction and prediction of protein structure (ref 2). 5. Sequence based methods to detect protein orthology and homology (ref 5).

该项目分为4个子项目： 1.用于改进多序列比对的迭代自动方法。目前构建CDD数据库的出发点是从SMART和PFAM等蛋白质家族模型中引入的多重比对。由于所有已知的多序列比对算法都不太完美，因此导入的比对存在错误，现在可以手动删除。该项目的目标是减少和简化这种手工工作（参考文献1）。 2.检测结构相似性的新方法。这个子项目的目标是开发新的方法来快速检测结构相似性，这将补充目前使用的方法（VAST）。因此，特别注意循环结构和索引方法的发展（参考文献7）。 3.基于序列和结构相似性的方法在研究蛋白质进化（和协同进化）中的应用。特别感兴趣的包括从序列共进化预测蛋白质相互作用（参考文献3，4，6）。 4.蛋白质结构的分类和预测（参考文献2）. 5.基于序列的方法来检测蛋白质的同源性和同源性（参考文献5）。

项目成果

Structural footprinting in protein structure comparison: the impact of structural fragments.

• DOI: 10.1186/1472-6807-7-53
• 发表时间: 2007-08-09
• 期刊: BMC structural biology
• 作者: Zotenko E;Dogan RI;Wilbur WJ;O'Leary DP;Przytycka TM
• 通讯作者: Przytycka TM

Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment.

• DOI: 10.1186/1471-2105-8-173
• 发表时间: 2007-05-23
• 期刊: BMC bioinformatics
• 影响因子: 3
• 作者: Jothi R;Przytycka TM;Aravind L
• 通讯作者: Aravind L