pSumo-CD: predicting sumoylation sites in proteins with covariance discriminant algorithm by incorporating sequence-coupled effects into general PseAAC
pSumo-CD: predicting sumoylation sites in proteins with covariance discriminant algorithm by incorporating sequence-coupled effects into general PseAAC
复制标题
pSumo-CD：通过将序列耦合效应纳入通用 PseAAC 中，使用协方差判别算法预测蛋白质中的 sumoylation 位点
DOI：
10.1093/bioinformatics/btw387
复制
发表时间：
2016-10-15
期刊：
影响因子：
5.8
通讯作者：
Chou, Kuo-Chen
中科院分区：
文献类型：
--
作者：
Jia, Jianhua;Zhang, Liuxia;Chou, Kuo-Chen
动机
Sumoylation 是一种翻译后修饰 (PTM) 过程，其中小的泛素相关修饰剂 (SUMO) 通过共价键连接到底物蛋白上。它对于许多不同的生物过程至关重要，例如复制基因组、表达基因、定位和稳定蛋白质；不幸的是，它还与许多主要疾病有关，包括阿尔茨海默病和帕金森病。因此，对于基础研究和药物开发来说，识别蛋白质中的苏酰化位点非常重要。
结果
为了解决这个问题，我们开发了一种名为 pSumo-CD 的预测器，将序列耦合信息合并到一般伪氨基酸组成（PseAAC）中，并引入协方差判别（CD）算法，其中引入了偏差调整项，具有自动调整由于训练数据不平衡而造成的偏差所造成的误差的功能。严格的交叉验证表明，出于相同目的，新的预测器明显优于现有的最先进的预测方法。
可用性和实施
为了方便大多数实验科学家，我们在 http://www.jci-bioinfo.cn/pSumo-CD 上建立了一个用户友好的 pSumo-CD 网络服务器，用户可以轻松地获得所需的结果，而无需通过涉及复杂的数学方程。
联系方式
jjia@gordonlifescience.org、xxiao@gordonlifescience.org 或 kcchou@gordonlifescience.org 补充信息：补充数据可在生物信息学在线获取。
MOTIVATION
Sumoylation is a post-translational modification (PTM) process, in which small ubiquitin-related modifier (SUMO) is attaching by covalent bonds to substrate protein. It is critical to many different biological processes such as replicating genome, expressing gene, localizing and stabilizing proteins; unfortunately, it is also involved with many major disorders including Alzheimer's and Parkinson's diseases. Therefore, for both basic research and drug development, it is important to identify the sumoylation sites in proteins.
RESULTS
To address such a problem, we developed a predictor called pSumo-CD by incorporating the sequence-coupled information into the general pseudo-amino acid composition (PseAAC) and introducing the covariance discriminant (CD) algorithm, in which a bias-adjustment term, which has the function to automatically adjust the errors caused by the bias due to the imbalance of training data, had been incorporated. Rigorous cross-validations indicated that the new predictor remarkably outperformed the existing state-of-the-art prediction method for the same purpose.
AVAILABILITY AND IMPLEMENTATION
For the convenience of most experimental scientists, a user-friendly web-server for pSumo-CD has been established at http://www.jci-bioinfo.cn/pSumo-CD, by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved.
CONTACT
jjia@gordonlifescience.org, xxiao@gordonlifescience.org or kcchou@gordonlifescience.orgSupplementary information: Supplementary data are available at Bioinformatics online.