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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
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Source Code for Biology and Medicine

ISSN: 1751-0473