Comput Biol Chem - Exploring the limits of fold discrimination by structural alignment: a large scale benchmark using decoys of known fold.

Tópicos

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Resumo

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.

Resumo Limpo

protein structur comparison pairwis align common use identifi high similar substructur pair protein provid measur structur similar base size geometr similar match score routin appli analys protein fold space assumpt high statist signific equival meaning relationship howev truth assumpt previous difficult test sinc lack autom method reli under principl resolut present method base use topolog descript global protein structur provid independ mean assess abil structur align maintain meaning structur correspond larg scale use larg set decoy specifi global fold benchmark three wide use method structur comparison sap tmalign dali test degre assumpt justifi method applic topolog edit distanc measur provid scale degre fold chang show broad correl high structur align score low edit distanc remain mani pair high signific score differ core strand swap therefor structur differ global level possibl caus problem mean present assess protein fold space discuss

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