Vriend G, Sander C
European Molecular Biology Laboratory, Heidelberg, Federal Republic of Germany.
Proteins. 1991;11(1):52-8. doi: 10.1002/prot.340110107.
We present a fully automatic algorithm for three-dimensional alignment of protein structures and for the detection of common substructures and structural repeats. Given two proteins, the algorithm first identifies all pairs of structurally similar fragments and subsequently clusters into larger units pairs of fragments that are compatible in three dimensions. The detection of similar substructures is independent of insertion/deletion penalties and can be chosen to be independent of the topology of loop connections and to allow for reversal of chain direction. Using distance geometry filters and other approximations, the algorithm, implemented in the WHAT IF program, is so fast that structural comparison of a single protein with the entire database of known protein structures can be performed routinely on a workstation. The method reproduces known non-trivial superpositions such as plastocyanin on azurin. In addition, we report surprising structural similarity between ubiquitin and a (2Fe-2S) ferredoxin.
我们提出了一种用于蛋白质结构三维比对以及检测常见子结构和结构重复序列的全自动算法。给定两个蛋白质，该算法首先识别所有结构相似片段对，随后将三维兼容的片段对聚类为更大的单元。相似子结构的检测与插入/缺失罚分无关，并且可以选择与环连接的拓扑结构无关，并允许链方向反转。使用距离几何滤波器和其他近似方法，在WHAT IF程序中实现的该算法速度非常快，以至于可以在工作站上常规地对单个蛋白质与已知蛋白质结构的整个数据库进行结构比较。该方法重现了已知的非平凡叠加，如质体蓝素与天青蛋白的叠加。此外，我们报告了泛素与一种（2Fe-2S）铁氧化还原蛋白之间惊人的结构相似性。
