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Table 4 Results over the final EVA test

From: PCI-SS: MISO dynamic nonlinear protein secondary structure prediction

 

Avg per residue

Avg per chain

Method

CC

Q 3

BAD

CC

Q 3

BAD

SOV

PHD

0.619

76.09

2.65

0.631

75.96

2.82

71.4

PHDpsi

0.619

76.09

2.65

0.631

75.96

2.82

71.4

PROF_king

0.577

72.65

3.70

0.594

72.86

3.38

66.8

PROFsec

0.651

77.72

2.36

0.659

77.70

2.49

75.3

PSIPRED-live (UniREF100 DB)

0.668

79.02

2.01

0.675

78.86

2.12

76.1

Sable

0.633

76.74

2.62

0.634

76.50

2.74

73.9

Sable2

0.651

77.95

1.86

0.644

77.45

2.05

73.0

SCRATCH (SSPro3)

0.616

76.07

3.24

0.622

76.15

3.20

70.6

SSPro4

0.643

77.69

2.43

0.642

77.58

2.46

72.0

Cascaded PCI

0.632

76.45

2.70

0.624

76.31

2.69

72.0

PSIPRED-local (frozen nr DB)

0.676

79.44

2.13

0.658

79.36

2.20

75.5

post-PCI(PCI &PSIPRED)

0.682

79.58

1.60

0.656

79.37

1.68

76.4

Bad-Score-Rule

0.679

79.59

1.98

0.659

79.45

2.10

75.7

  1. Results over the final EVA test set of 125 new protein chains dissimilar to all training data. CC denotes the average Matthews' correlation coefficient observed for the three classes. 'Avg per residue' results are calculated over the pool of all residues in the dataset whereas 'Avg per chain' results are compiled for each chain prior to computing the average. PSIPRED-local refers to the output of PSIPRED v2.45 run locally when provided with PSSM data generated from the filtered NCBI non-redundant nr database as frozen on 3 May 2004. PSIPRED-live indicates the performance of the actual PSIPRED server [31] as of the day that each protein chain was added to the EVA system. Bad-Score-Rule in the last row shows the results when a rule is applied to combine postPCI with PSIPRED to optimize Q3 score at the cost of BAD score (see text for details).