College of Science, China Agricultural University, Beijing 100083, People's Republic of China.
Protein Eng Des Sel. 2009 Nov;22(11):707-12. doi: 10.1093/protein/gzp055. Epub 2009 Sep 25.
Palmitoylation is an important hydrophobic protein modification activity that participates many cellular processes, including signaling, neuronal transmission, membrane trafficking and so on. So it is an important problem to identify palmitoylated proteins and the corresponding sites. Comparing with the expensive and time-consuming biochemical experiments, the computational methods have attracted much attention due to their good performances in predicting palmitoylation sites. In this paper, we develop a novel automated computational method to perform this work. For a sequence segment in a given protein, the encoding scheme based on the composition of k-spaced amino acid pairs (CKSAAP) is introduced, and then the support vector machine is used as the predictor. The proposed prediction model CKSAAP-Palm outperforms the existing method CSS-Palm2.0 on both cross-validation experiments and some independent testing data sets. These results imply that our CKSAAP-Palm is able to predict more potential palmitoylation sites and increases research productivity in palmitoylation sites discovery. The corresponding software can be freely downloaded from http://www.aporc.org/doc/wiki/CKSAAP-Palm.
棕榈酰化是一种重要的疏水性蛋白质修饰活性，参与许多细胞过程，包括信号转导、神经元传递、膜运输等。因此，鉴定棕榈酰化蛋白和相应的位点是一个重要的问题。与昂贵且耗时的生化实验相比，由于在预测棕榈酰化位点方面的出色表现，计算方法引起了广泛关注。在本文中，我们开发了一种新颖的自动化计算方法来完成这项工作。对于给定蛋白质中的序列片段，引入了基于 k 间隔氨基酸对组成的编码方案（CKSAAP），然后使用支持向量机作为预测器。所提出的预测模型 CKSAAP-Palm 在交叉验证实验和一些独立测试数据集上均优于现有方法 CSS-Palm2.0。这些结果表明，我们的 CKSAAP-Palm 能够预测更多潜在的棕榈酰化位点，提高棕榈酰化位点发现的研究效率。相应的软件可从 http://www.aporc.org/doc/wiki/CKSAAP-Palm 免费下载。
