Assigning new GO annotations to protein data bank sequences by combinling structure and sequence homology
Assigning new GO annotations to protein data bank sequences by combinling structure and sequence homology
复制标题
DOI：
10.1002/prot.20355
复制
发表时间：
2005-03-01
影响因子：
2.9
通讯作者：
Shindyalov, IN
中科院分区：
文献类型：
--
作者：
Ponomarenko, JV;Bourne, PE;Shindyalov, IN
随着蛋白质数量的增加，需要提供高度准确且一致的功能注释。 Gene Ontology(TM) (GO) 以计算机可读和可用的形式提供一致的注释；因此，基于直接实验证据并通过序列同源性确定的推断，GO注释（GOA）已被分配给大量蛋白质序列。在这里，我们表明，对于蛋白质结构可用的情况，可以扩展和纠正该注释。具体来说，使用组合扩展（CE）算法进行结构比较，我们扩展了欧洲生物信息学研究所（EBI）GOA目前提供的蛋白质注释，以进一步描述蛋白质数据库（PDB）的内容。给出了通过该方法得出的生物学上有趣的注释的具体案例。鉴于序列、结构和功能之间的关系很复杂，我们探讨了这种关系对分配GOA的影响。考虑了超折叠（具有多种功能的折叠）的影响，并与蛋白质结构分类 (SCOP) 进行比较，考虑了家族、超家族和折叠的个体影响。 (C) 2005 Wiley-Liss, Inc.
Accompanying the discovery of an increasing number of proteins, there is the need to provide functional annotation that is both highly accurate and consistent. The Gene Ontology(TM) (GO) provides consistent annotation in a computer readable and usable form; hence, GO annotation (GOA) has been assigned to a large number of protein sequences based on direct experimental evidence and through inference determined by sequence homology. Here we show that this annotation can be extended and corrected for cases where protein structures are available. Specifically, using the Combinatorial Extension (CE) algorithm for structure comparison, we extend the protein annotation currently provided by GOA at the European Bioinformatics Institute (EBI) to further describe the contents of the Protein Data Bank (PDB). Specific cases of biologically interesting annotations derived by this method are given. Given that the relationship between sequence, structure, and function is complicated, we explore the impact of this relationship on assigning GOA. The effect of superfolds (folds with many functions) is considered and, by comparison to the Structural Classification of Proteins (SCOP), the individual effects of family, superfamily, and fold. (C) 2005 Wiley-Liss, Inc.