Program in Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, 92037 La Jolla, CA, USA.
BMC Bioinformatics. 2014 Apr 27;15:119. doi: 10.1186/1471-2105-15-119.
Periodic proteins, characterized by the presence of multiple repeats of short motifs, form an interesting and seldom-studied group. Due to often extreme divergence in sequence, detection and analysis of such motifs is performed more reliably on the structural level. Yet, few algorithms have been developed for the detection and analysis of structures of periodic proteins.
ConSole recognizes modularity in protein contact maps, allowing for precise identification of repeats in solenoid protein structures, an important subgroup of periodic proteins. Tests on benchmarks show that ConSole has higher recognition accuracy as compared to Raphael, the only other publicly available solenoid structure detection tool. As a next step of ConSole analysis, we show how detection of solenoid repeats in structures can be used to improve sequence recognition of these motifs and to detect subtle irregularities of repeat lengths in three solenoid protein families.
The ConSole algorithm provides a fast and accurate tool to recognize solenoid protein structures as a whole and to identify individual solenoid repeat units from a structure. ConSole is available as a web-based, interactive server and is available for download at http://console.sanfordburnham.org.
周期性蛋白的特征是存在多个短基序的重复，它们形成了一个有趣且很少被研究的群体。由于序列通常存在极端的差异，因此更可靠地在结构水平上进行此类基序的检测和分析。然而，已经开发出用于检测和分析周期性蛋白结构的算法却很少。
ConSole 识别蛋白质接触图中的模块性，允许精确识别螺旋蛋白结构中的重复，这是周期性蛋白的一个重要亚群。在基准测试上的测试表明，ConSole 的识别准确性比 Raphael 更高，Raphael 是唯一另一个可用的公开螺旋结构检测工具。作为 ConSole 分析的下一步，我们展示了如何在结构中检测螺旋重复，以改进这些基序的序列识别，并检测三个螺旋蛋白家族中重复长度的细微不规则性。
ConSole 算法提供了一种快速而准确的工具，可用于整体识别螺旋蛋白结构，并从结构中识别单个螺旋重复单元。ConSole 可作为基于网络的交互式服务器使用，并可在 http://console.sanfordburnham.org 上下载。
