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Table 1 Examples of assessment of secondary structure predictions using Q3, SOV’99, and SOV_refine (λ = 1)

From: SOV_refine: A further refined definition of segment overlap score and its significance for protein structure similarity

Index Sequence Q3 SOV’99 SOV_refine (λ = 1)
Reference CHHHHHHHHHHC
Predicted 1 CHCHCHCHCHCC 0.583 0.125 0.149
Predicted 2 CHHHCHHHCHHC 0.833 0.406 0.371
Predicted 3 CHHCCHHHHHCC 0.75 0.523 0.464
Predicted 4 CCCHHHHCCCCC 0.50 0.544 0.459
Predicted 5 CCCHHHHHCCCC 0.583 0.632 0.567
Predicted 6 CCCHHHHHHCCC 0.667 0.806 0.678
Predicted 7 CCCHHHHHHHCC 0.75 0.903 0.797
Predicted 8 CCCHHHHHHHHC 0.833 0.944 0.937
  1. Notice that predicted 3 and 4 indicate another different feature between SOV’99 and SOV_refine. Predicted 3 correctly predicts seven helices (in two segments) while Predicted 4 correctly predicts four helices (in one segment). In this situation, SOV_refine assigns a higher score to predicted 3 as seven correct helices are more consistent to the reference’s 10 helices compared to predicted 4’s four helices. However, SOV’99 in this case assigns a higher score to predicted 4 showing it prefers one segment prediction even though the number of accurately predicted residues is largely different