Enhanced fold recognition using efficient short fragment clustering.
Enhanced fold recognition using efficient short fragment clustering.
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发表时间：
2012-06
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通讯作者：
E. Krissinel
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作者：
E. Krissinel
CCP4软件套件中的主结构比对器SSM（二级结构匹配）在结构解析过程的中间阶段具有有限的适用性，此时二级结构由于结构不完整或主链碎片而无法可靠地计算。在这项研究中，我们描述了一种新的算法的比对和比较的蛋白质结构在CCP4，这是为了克服SSM的局限性，但保留其质量和速度。新算法名为GESAMT（General Efficient Structural Alignment of Macromolecular Targets），采用了从一组有希望的局部相似短片段中推导出全局结构相似性的旧思想，但使用了一些技术解决方案，使其速度大大加快。比较灵敏度和选择性分析显示，新算法的折叠识别性能有了意想不到的显著改善，这也使其在结构生物信息学领域的应用非常有用。从6.3版开始，新工具包含在CCP4软件套件中。
The main structure aligner in the CCP4 Software Suite, SSM (Secondary Structure Matching) has a limited applicability on the intermediate stages of the structure solution process, when the secondary structure cannot be reliably computed due to structural incompleteness or a fragmented mainchain. In this study, we describe a new algorithm for the alignment and comparison of protein structures in CCP4, which was designed to overcome SSM's limitations but retain its quality and speed. The new algorithm, named GESAMT (General Efficient Structural Alignment of Macromolecular Targets), employs the old idea of deriving the global structure similarity from a promising set of locally similar short fragments, but uses a few technical solutions that make it considerably faster. A comparative sensitivity and selectivity analysis revealed an unexpected significant improvement in the fold recognition properties of the new algorithm, which also makes it useful for applications in the structural bioinformatics domain. The new tool is included in the CCP4 Software Suite starting from version 6.3.