Biological Assembly Comparison with VAST

Methods Mol Biol. 2020;2112:175-186. doi: 10.1007/978-1-0716-0270-6_13.

Abstract

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.

Keywords: Molecular assembly; Protein complex; Secondary structure element; Structure alignment; Structure comparison.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Intramural

MeSH terms

  • Algorithms
  • Databases, Protein
  • Monte Carlo Method
  • Protein Conformation
  • Proteins / chemistry*
  • Search Engine / methods
  • Sequence Alignment / methods*
  • Software

Substances

  • Proteins