National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Methods Mol Biol. 2020;2112:175-186. doi: 10.1007/978-1-0716-0270-6_13.
The VAST+ algorithm is an efficient, simple, and elegant solution to the problem of comparing the atomic structures of biological assemblies. Given two protein assemblies, it takes as input all the pairwise structural alignments of the component proteins. It then clusters the rotation matrices from the pairwise superpositions, with the clusters corresponding to subsets of the two assemblies that may be aligned and well superposed. It uses the Vector Alignment Search Tool (VAST) protein-protein comparison method for the input structural alignments, but other methods could be used, as well. From a chosen cluster, an "original" alignment for the assembly may be defined by simply combining the relevant input alignments. However, it is often useful to reduce/trim the original alignment, using a Monte Carlo refinement algorithm, which allows biologically relevant conformational differences to be more readily detected and observed. The method is easily extended to include RNA or DNA molecules. VAST+ results may be accessed via the URL https://www.ncbi.nlm.nih.gov/Structure , then entering a PDB accession or terms in the search box, and using the link [VAST+] in the upper right corner of the Structure Summary page.
VAST+ 算法是一种高效、简单且优雅的解决方案，用于比较生物组装体的原子结构。给定两个蛋白质组装体，它将所有组件蛋白质的两两结构比对作为输入。然后，它对来自两两叠加的旋转矩阵进行聚类，聚类对应于两个组装体中可能对齐且良好叠加的子集。它使用 Vector Alignment Search Tool（VAST）蛋白-蛋白比较方法进行输入结构比对，但也可以使用其他方法。从选择的聚类中，可以通过简单地组合相关的输入比对来定义组装体的“原始”比对。然而，使用蒙特卡罗精修算法来减少/修剪原始比对通常是有用的，这允许更轻松地检测和观察生物相关的构象差异。该方法易于扩展到包括 RNA 或 DNA 分子。可以通过 URL https://www.ncbi.nlm.nih.gov/Structure 访问 VAST+ 结果，然后在搜索框中输入 PDB 访问号或术语，并使用 Structure Summary 页面右上角的链接 [VAST+]。
