Prediction of ubiquitination sites by using the composition of k-spaced amino acid pairs.
Prediction of ubiquitination sites by using the composition of k-spaced amino acid pairs.
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利用 k 间隔氨基酸对的组成预测泛素化位点
DOI：
10.1371/journal.pone.0022930
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发表时间：
2011
期刊：
影响因子：
3.7
通讯作者：
Zhang Z
中科院分区：
文献类型：
--
作者：
Chen Z;Chen YZ;Wang XF;Wang C;Yan RX;Zhang Z
泛素化作为蛋白质翻译后最重要的可逆修饰之一，已被报道参与多种生物学过程，并与多种疾病密切相关。要完全破译泛素化相关生物过程的分子机制，首先但也是关键的一步是识别泛素化底物和相应的泛素化位点。在这里，开发了一个新的生物信息学工具CKSAAP_UbSite来预测蛋白质序列中的泛素化位点。在支持向量机的辅助下，CKSAAP_UbSite的突出之处在于使用围绕查询站点(即查询序列中的任何赖氨酸)的k间隔氨基酸对的组合作为输入。在酵母泛素化位点数据集(Radivojac et al，Proteins，2010，78：365-380)上进行训练和测试时，对1：1的阳性和阴性样本进行了100倍交叉验证，结果表明CKSAAP_UbSite的准确率和最小预测误差分别达到73.40%和0.4694。建议的CKSAAP_UbSite也进行了密集的基准测试，表现出比一些现有预测指标更好的性能，这表明它可以作为一个有用的工具提供给社区。目前，CKSAAPUBSITE可在http://protein.cau.edu.cn/cksaap_ubsite/.免费访问此外，我们还发现泛素化位点周围的序列模式在不同物种之间并不保守。为了保证合理的预测性能，目前的CKSAAP_UbSite的应用应局限于酵母蛋白质组。
As one of the most important reversible protein post-translation modifications, ubiquitination has been reported to be involved in lots of biological processes and closely implicated with various diseases. To fully decipher the molecular mechanisms of ubiquitination-related biological processes, an initial but crucial step is the recognition of ubiquitylated substrates and the corresponding ubiquitination sites. Here, a new bioinformatics tool named CKSAAP_UbSite was developed to predict ubiquitination sites from protein sequences. With the assistance of Support Vector Machine (SVM), the highlight of CKSAAP_UbSite is to employ the composition of k-spaced amino acid pairs surrounding a query site (i.e. any lysine in a query sequence) as input. When trained and tested in the dataset of yeast ubiquitination sites (Radivojac et al, Proteins, 2010, 78: 365–380), a 100-fold cross-validation on a 1∶1 ratio of positive and negative samples revealed that the accuracy and MCC of CKSAAP_UbSite reached 73.40% and 0.4694, respectively. The proposed CKSAAP_UbSite has also been intensively benchmarked to exhibit better performance than some existing predictors, suggesting that it can be served as a useful tool to the community. Currently, CKSAAP_UbSite is freely accessible at http://protein.cau.edu.cn/cksaap_ubsite/. Moreover, we also found that the sequence patterns around ubiquitination sites are not conserved across different species. To ensure a reasonable prediction performance, the application of the current CKSAAP_UbSite should be limited to the proteome of yeast.
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影响因子：
2.9
作者：
Radivojac, Predrag;Vacic, Vladimir;Haynes, Chad;Cocklin, Ross R.;Mohan, Amrita;Heyen, Joshua W.;Goebl, Mark G.;Iakoucheva, Lilia M.
通讯作者：
Iakoucheva, Lilia M.
DOI：
10.1016/s0097-8485(96)80004-0
发表时间：
1996-03-01
期刊：
COMPUTERS & CHEMISTRY
影响因子：
--
作者：
Gribskov, M;Robinson, NL
通讯作者：
Robinson, NL
影响因子：
9.8
作者：
Neduva V;Linding R;Su-Angrand I;Stark A;de Masi F;Gibson TJ;Lewis J;Serrano L;Russell RB
通讯作者：
Russell RB
影响因子：
16
作者：
Pickart, CM
通讯作者：
Pickart, CM
影响因子：
3.7
作者：
Shao J;Xu D;Tsai SN;Wang Y;Ngai SM
通讯作者：
Ngai SM