Scan2S: Increasing the precision of PROSITE pattern motifs using secondary structure constraints
Scan2S: Increasing the precision of PROSITE pattern motifs using secondary structure constraints
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DOI：
10.1002/prot.22008
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发表时间：
2008-09-01
影响因子：
2.9
通讯作者：
Niv，Masha Y.
中科院分区：
文献类型：
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作者：
Skrabanek，Lucy;Niv，Masha Y.
序列特征数据库，如PROSITE，包括指示蛋白质功能的蛋白质模式基序，广泛用于功能预测研究，细胞定位注释和序列分类。正确的标注依赖于对母题的高精度标注。我们提出了一种新的通用方法，通过包括二级结构约束（ssc）来提高已建立的蛋白质模式基序的精度。我们使用Scan2S，第一个序列基序扫描程序，可选地包括ssc，以增加PROSITE模式基序。约束来源于DSSP二级结构分配或PSIPRED对PROSITE记录的真阳性命中的预测。针对所有SwissProt序列扫描二级结构增强基序，并预先计算二级结构预测。在此数据集上，PSIPRED衍生ssc的基序比DSSP衍生约束的基序表现出更好的性能。782个PSIPRED增强基序中，763个基序的精度与原始基序相比保持不变或提高；26个图案的绝对精度提高了10-30%。我们在http://physiology.med.cornell.edu/go/scan2s上提供了完整的增强图案和Scan2S程序。我们的结果提出了一种通过包含ssc来提高蛋白质模式检测精度的通用方案。2008的蛋白质。©2008 Wiley‐Liss, Inc。
Sequence signature databases such as PROSITE, which include protein pattern motifs indicative of a protein's function, are widely used for function prediction studies, cellular localization annotation, and sequence classification. Correct annotation relies on high precision of the motifs. We present a new and general approach for increasing the precision of established protein pattern motifs by including secondary structure constraints (SSCs). We use Scan2S, the first sequence motif‐scanning program to optionally include SSCs, to augment PROSITE pattern motifs. The constraints were derived from either the DSSP secondary structure assignment or the PSIPRED predictions for PROSITE‐documented true positive hits. The secondary structure‐augmented motifs were scanned against all SwissProt sequences, for which secondary structure predictions were precalculated. Against this dataset, motifs with PSIPRED‐derived SSCs exhibited improved performance over motifs with DSSP‐derived constraints. The precision of 763 of the 782 PSIPRED‐augmented motifs remained unchanged or increased compared to the original motifs; 26 motifs showed an absolute precision increase of 10–30%. We provide the complete set of augmented motifs and the Scan2S program at http://physiology.med.cornell.edu/go/scan2s. Our results suggest a general protocol for increasing the precision of protein pattern detection via the inclusion of SSCs. Proteins 2008. © 2008 Wiley‐Liss, Inc.