Exploring the limits of fold discrimination by structural alignment: A large scale benchmark using decoys of known fold

[Display omitted] ► Structure alignment methods are used to assign proteins to fold groups. ► The accuracy of this procedure is difficult to test as the definition of folds can be debated. ► By defining folds topologically and building decoys with defined fold the accuracy of fold assignments can be tested. ► Protein structure alignments decoys of different fold can be assigned a high significance, leading to errors in fold classification. ► This observation can be extended to comparisons between decoy models and real protein structures. Protein structure comparison by pairwise alignment is commonly used to identify highly similar substructures in pairs of proteins and provide a measure of structural similarity based on the size and geometric similarity of the match. These scores are routinely applied in analyses of protein fold space under the assumption that high statistical significance is equivalent to a meaningful relationship, however the truth of this assumption has previously been difficult to test since there is a lack of automated methods which do not rely on the same underlying principles. As a resolution to this we present a method based on the use of topological descriptions of global protein structure, providing an independent means to assess the ability of structural alignment to maintain meaningful structural correspondances on a large scale. Using a large set of decoys of specified global fold we benchmark three widely used methods for structure comparison, SAP, TM-align and DALI, and test the degree to which this assumption is justified for these methods. Application of a topological edit distance measure to provide a scale of the degree of fold change shows that while there is a broad correlation between high structural alignment scores and low edit distances there remain many pairs of highly significant score which differ by core strand swaps and therefore are structurally different on a global level. Possible causes of this problem and its meaning for present assessments of protein fold space are discussed.