Identification of function-associated loop motifs and application to protein function prediction
Identification of function-associated loop motifs and application to protein function prediction
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DOI：
10.1093/bioinformatics/btl382
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发表时间：
2006-09-15
期刊：
影响因子：
5.8
通讯作者：
Oliva, Baldo
中科院分区：
文献类型：
--
作者：
Espadaler, Jordi;Querol, Enrique;Oliva, Baldo
动机：蛋白质结构中功能相关的局部3D基序的检测可以在缺乏序列或折叠相似性的情况下提供对蛋白质功能的见解。已知蛋白质环在蛋白质功能中起重要作用，并且已经描述了几种环分类，但是在这种分类中推定的功能性3D基序的自动识别尚未得到解决。这种识别可以用于序列annotations.Results：我们评估了三种不同的评分方法，他们的能力，以确定已知的基序从PROSITE数据库中的ArchDB。超过500个新的推定的功能相关的基序没有在PROSITE的报告被确定。来自这些基序的序列模式在预测精确注释方面特别有用。相对于标准BLAST，可靠序列注释的数量可以增加高达100%。
Motivation: The detection of function-related local 3D-motifs in protein structures can provide insights towards protein function in absence of sequence or fold similarity. Protein loops are known to play important roles in protein function and several loop classifications have been described, but the automated identification of putative functional 3D-motifs in such classifications has not yet been addressed. This identification can be used on sequence annotations.Results: We evaluated three different scoring methods for their ability to identify known motifs from the PROSITE database in ArchDB. More than 500 new putative function-related motifs not reported in PROSITE were identified. Sequence patterns derived from these motifs were especially useful at predicting precise annotations. The number of reliable sequence annotations could be increased up to 100% with respect to standard BLAST.