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Table 5 Performance of individual and combination scoring functions on six decoy sets.

From: A comprehensive analysis of 40 blind protein structure predictions

Scoring function

RMSD range (Ã…) (average)

Percentage ≤ 6.0 Å (average)

Initial

3.8 – 14.4

9.3

Density

3.9 – 12.1

12.3

Hydrophobic compactness

4.1 – 13.8

10.1

All-atom pairwise

4.1 – 14.1

11.0

Electrostatics

5.2 – 14.4

4.2

Van der Waals

5.6 – 13.1

3.9

Secondary structure match

4.5 – 10.1

10.2

Combined

3.9 – 13.2

14.1

Random

6.6 – 12.1

0.5

  1. Each function reduces a sample of 10,000 conformations to 1000 for which the Cα RMSD range and the percentage of conformations within 6.0 Å Cα RMSD are given. The "Initial" row represents the initial distribution (generated by the method corresponding to the last entry in Table 4). The "Random" function simply selects an arbitrary 1000 conformations from the pool of 10,000 for each protein. The best results are achieved using the combined function.