Exclusion from the training set of test-set similar proteins results in significantly reduced scoring function performance (Fig. ). There is a significant drop in the performance of all scoring functions even when a sequence identity cutoff of 100% is imposed, i.e. when only proteins with identical sequence to those in the test set are excluded from the training set. Reducing the sequence identity cutoff from 90% to 50% has a smaller impact on performance than the initial imposition of a 100% cutoff.