We propose a novel method for scoring the accuracy of
protein binding site predictions β the Binding-site Distance Test
(BDT) score. Recently, the Matthews Correlation Coefficient (MCC)
has been used to evaluate binding site predictions, both by developers
of new methods and by the assessors for the community wide
prediction experiment β CASP8. Whilst being a rigorous scoring
method, the MCC does not take into account the actual 3D location
of the predicted residues from the observed binding site. Thus, an
incorrectly predicted site that is nevertheless close to the observed
binding site will obtain an identical score to the same number of nonbinding
residues predicted at random. The MCC is somewhat affected
by the subjectivity of determining observed binding residues
and the ambiguity of choosing distance cutoffs. By contrast the BDT
method produces continuous scores ranging between 0 and 1, relating
to the distance between the predicted and observed residues.
Residues predicted close to the binding site will score higher than
those more distant, providing a better reflection of the true accuracy
of predictions. The CASP8 function predictions were evaluated using
both the MCC and BDT methods and the scores were compared.
The BDT was found to strongly correlate with the MCC
scores whilst also being less susceptible to the subjectivity of defining
binding residues. We therefore suggest that this new simple
score is a potentially more robust method for future evaluations of
protein-ligand binding site predictions
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