Department of Chemistry, Tongji University, 1239 Siping Road, Shanghai 200092, China.
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W298-302. doi: 10.1093/nar/gks361. Epub 2012 May 2.
Many studies have demonstrated that shape string is an extremely important structure representation, since it is more complete than the classical secondary structure. The shape string provides detailed information also in the regions denoted random coil. But few services are provided for systematic analysis of protein shape string. To fill this gap, we have developed an accurate shape string predictor based on two innovative technologies: a knowledge-driven sequence alignment and a sequence shape string profile method. The performance on blind test data demonstrates that the proposed method can be used for accurate prediction of protein shape string. The DSP server provides both predicted shape string and sequence shape string profile for each query sequence. Using this information, the users can compare protein structure or display protein evolution in shape string space. The DSP server is available at both http://cheminfo.tongji.edu.cn/dsp/ and its main mirror http://chemcenter.tongji.edu.cn/dsp/.
许多研究表明，形状字符串是一种极其重要的结构表示，因为它比经典的二级结构更完整。形状字符串还提供了无规卷曲区域的详细信息。但是，很少有服务可以提供用于蛋白质形状字符串的系统分析。为了填补这一空白，我们开发了一种基于两种创新技术的准确形状字符串预测器：知识驱动的序列比对和序列形状字符串轮廓方法。盲测数据的性能表明，该方法可用于准确预测蛋白质形状字符串。DSP 服务器为每个查询序列提供预测的形状字符串和序列形状字符串轮廓。使用这些信息，用户可以比较蛋白质结构或在形状字符串空间中显示蛋白质进化。DSP 服务器可在 http://cheminfo.tongji.edu.cn/dsp/ 和其主镜像 http://chemcenter.tongji.edu.cn/dsp/ 上使用。
