Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China.
PLoS One. 2011 Apr 20;6(4):e19001. doi: 10.1371/journal.pone.0019001.
As one of the most essential post-translational modifications (PTMs) of proteins, proteolysis, especially calpain-mediated cleavage, plays an important role in many biological processes, including cell death/apoptosis, cytoskeletal remodeling, and the cell cycle. Experimental identification of calpain targets with bona fide cleavage sites is fundamental for dissecting the molecular mechanisms and biological roles of calpain cleavage. In contrast to time-consuming and labor-intensive experimental approaches, computational prediction of calpain cleavage sites might more cheaply and readily provide useful information for further experimental investigation. In this work, we constructed a novel software package of GPS-CCD (Calpain Cleavage Detector) for the prediction of calpain cleavage sites, with an accuracy of 89.98%, sensitivity of 60.87% and specificity of 90.07%. With this software, we annotated potential calpain cleavage sites for hundreds of calpain substrates, for which the exact cleavage sites had not been previously determined. In this regard, GPS-CCD 1.0 is considered to be a useful tool for experimentalists. The online service and local packages of GPS-CCD 1.0 were implemented in JAVA and are freely available at: http://ccd.biocuckoo.org/.
作为蛋白质翻译后修饰（PTMs）中最重要的一种，蛋白水解（尤其是钙蛋白酶介导的切割）在许多生物学过程中起着重要作用，包括细胞死亡/凋亡、细胞骨架重塑和细胞周期。具有真正切割位点的钙蛋白酶靶标的实验鉴定对于剖析钙蛋白酶切割的分子机制和生物学作用至关重要。与耗时且费力的实验方法相比，钙蛋白酶切割位点的计算预测可能更便宜、更容易为进一步的实验研究提供有用信息。在这项工作中，我们构建了一个新的 GPS-CCD（钙蛋白酶切割检测器）软件包，用于预测钙蛋白酶切割位点，其准确性为 89.98%，灵敏度为 60.87%，特异性为 90.07%。有了这个软件，我们为数百种钙蛋白酶底物注释了潜在的钙蛋白酶切割位点，这些底物以前没有确定过确切的切割位点。在这方面，GPS-CCD 1.0 被认为是实验者的有用工具。GPS-CCD 1.0 的在线服务和本地软件包是用 JAVA 实现的，可以在以下网址免费获取：http://ccd.biocuckoo.org/。
