Table 5 Comparison of the predictive performance of Pep-3D-Search with different distance parameters (AHA).

AHA (distance threshold = 3.7)

TP/PE

17/20

7/16

12/44

11/34

17/36*

6/32

6/25*

9/33

13/36

8/32

MCC

0.375

0.1243

0.1716

0.2286

0.1565

0.0733

0.0595

0.1502

0.2855

0.0351

0.1659

Sensitivity

0.85

0.4375

0.2727

0.3235

0.4722

0.1875

0.24

0.2727

0.3611

0.25

0.3667

Precision

0.8095

0.3684

0.8

1.0

0.85

0.375

0.4

0.6

0.8125

0.3333

0.6349

AHA (distance threshold = 4)

TP/PE

16/20

7/10

13/42

8/30

15/30*

5/39

6/23

10/37

12/35

10/34

MCC

0.3491

0.1528

0.1887

0.1584

0.1379

0.0283

0.0598

0.1695

0.2525

0.0858

0.1583

Sensitivity

0.8

0.7

0.3095

0.2667

0.5

0.1282

0.2609

0.2703

0.3429

0.2941

0.3873

Precision

0.7619

0.3684

0.8667

0.7273

0.75

0.3125

0.4

0.6667

0.75

0.4167

0.6021

AHA (distance threshold = 4.3)

TP/PE

16/18

8/11

14/42

8/36

17/30*

9/37

4/16*

11/37

10/33

4/26

MCC

0.3537

0.1773

0.2052

0.1558

0.1571

0.1431

0.0394

0.1923

0.1869

-0.0514

0.1559

Sensitivity

0.8889

0.7273

0.3333

0.2222

0.5667

0.2432

0.25

0.2973

0.303

0.1538

0.3986

Precision

0.7619

0.4211

0.9333

0.7273

0.85

0.5625

0.2667

0.7333

0.625

0.1667

0.6048

AHA (distance threshold = 4.6)

TP/PE

19/36

9/24

9/44

4/41

18/38

0/34

8/25*

8/36*

5/37

6/27

MCC

0.3989

0.1483

0.1206

0.0495

0.1663

-0.1023

0.0813

0.1241

-0.0357

0.0051

0.0956

Sensitivity

0.5278

0.375

0.2045

0.0976

0.4737

0.0

0.32

0.2222

0.1351

0.2222

0.2578

Precision

0.9048

0.4737

0.6

0.3636

0.9

0.0

0.5333

0.5333

0.3125

0.25

0.4871