STRIKE: evaluation of protein MSAs using a single 3D structure

Result: We developed STRIKE, a method that determines the relative accuracy of two alternative alignments of the same sequences using a single structure. We validated our methodology on three commonly used reference datasets (BAliBASE, Homestrad and Prefab). Given two alignments, STRIKE manages to identify the most accurate one in 70% of the cases on average. This figure increases to 79% when considering very challenging datasets like the RV11 category of BAliBASE. This discrimination capacity is significantly higher than that reported for other metrics such as Contact Accepted mutation or Blosum. We show that this increased performance results both from a refined definition of the contacts and from the use of an improved contact substitution score.