Protein structure alignments and structural similarity score code for: Benchmarking methods of protein structure alignment

The function of a protein is primarily determined by its structure and amino acid sequence. Many biological questions of interest rely on being able to accurately determine the group of structures to which domains of a protein belong (often referred to as their `fold'); this can be done through alignment and comparison of protein structures. This fundamental task underpins predicting function, identification of homology, and testing hypotheses about the way \"protein-space'' is organised. Dozens of different methods for Protein Structure Alignment (PSA) have been proposed that use a wide range of techniques.   The aim of this study is to determine the ability of PSA methods to identify pairs of protein domains known to share differing levels of structural similarity, and to assess their utility for clustering domains from several different folds into known groups. 

We present the results of a comprehensive investigation into eighteen PSA methods; to our knowledge this is the largest p...