Shu Nanjiang, Hovmöller Sven, Zhou Tuping
Structural Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden.
Curr Protein Pept Sci. 2008 Aug;9(4):310-24. doi: 10.2174/138920308785132703.
Different methods for describing and comparing the structures of the tens of thousands of proteins that have been determined by X-ray crystallography are reviewed. Such comparisons are important for understanding the structures and functions of proteins and facilitating structure prediction, as well as assessing structure prediction methods. We summarize methods in this field emphasizing ways of representing protein structures as one-dimensional geometrical strings. Such strings are based on the shape symbols of clustered regions of phi/Psi dihedral angle pairs of the polypeptide backbones as described by the Ramachandran plot. These one-dimensional expressions are as compact as secondary structure description but contain more information in loop regions. They can be used for fast searching for similar structures in databases and for comparing similarities between proteins and between the predicted and native structures.
本文综述了用于描述和比较通过X射线晶体学测定的数以万计蛋白质结构的不同方法。此类比较对于理解蛋白质的结构与功能、促进结构预测以及评估结构预测方法都很重要。我们总结了该领域的方法，重点介绍了将蛋白质结构表示为一维几何字符串的方式。此类字符串基于拉马钱德兰图所描述的多肽主链φ/ψ二面角对聚类区域的形状符号。这些一维表达式与二级结构描述一样紧凑，但在环区包含更多信息。它们可用于在数据库中快速搜索相似结构，以及比较蛋白质之间以及预测结构与天然结构之间的相似性。
