Skip to main content

Table 5 Leave-cluster-out cross validation results of the four models on the 23 protein families (A to W) and 3 multi-family (X to Z) clusters of PDBbind v2009 refined set (N = 1740) in terms of root mean square error RMSE, standard deviation SD in linear correlation, Pearson correlation coefficient Rp and Spearman correlation coefficient Rs

From: Substituting random forest for multiple linear regression improves binding affinity prediction of scoring functions: Cyscore as a case study

     

MLR::Cyscore

   

RF::Cyscore

   

RF::CyscoreVina

   

RF::CyscoreVinaElem

 

Cluster name

Cluster

N

RMSE

SD

Rp

Rs

RMSE

SD

Rp

Rs

RMSE

SD

Rp

Rs

RMSE

SD

Rp

Rs

HIV protease

A

188

1.65

1.53

0.259

0.216

1.70

1.51

0.310

0.201

1.76

1.56

0.182

0.105

1.77

1.56

0.166

0.129

trypsin

B

74

1.24

1.11

0.612

0.695

1.10

1.11

0.610

0.636

0.96

0.97

0.723

0.700

0.93

0.93

0.751

0.715

carbonic anhydrase

C

57

2.47

1.35

0.473

0.343

2.44

1.43

0.368

0.264

2.60

1.37

0.448

0.372

2.33

1.35

0.481

0.234

thrombin

D

53

1.52

1.40

0.702

0.676

1.50

1.44

0.680

0.611

1.47

1.45

0.675

0.675

1.46

1.40

0.699

0.680

protein tyrosine phosphatase

E

32

1.23

1.06

0.411

0.313

1.30

1.10

0.338

0.268

1.36

0.98

0.538

0.542

1.23

0.89

0.643

0.615

factor Xa

F

32

1.18

0.96

0.604

0.634

1.54

1.13

0.367

0.356

1.53

1.02

0.533

0.498

1.61

1.07

0.470

0.470

urokinase

G

29

1.15

1.14

0.643

0.602

1.10

1.14

0.642

0.645

1.25

1.27

0.516

0.436

1.05

1.06

0.699

0.624

different similar transporters

H

29

0.96

0.96

0.285

0.122

1.27

0.99

0.056

-0.040

1.10

0.98

0.188

0.077

1.01

0.93

0.354

0.123

c-AMP dependent kinase

I

17

1.32

1.15

0.537

0.537

1.16

1.11

0.582

0.602

0.94

0.91

0.748

0.664

1.06

0.91

0.747

0.644

β-glucosidase

J

17

1.03

0.78

0.383

0.316

1.04

0.76

0.444

0.365

0.92

0.72

0.518

0.443

1.05

0.68

0.597

0.649

antibodies

K

16

1.41

1.43

0.693

0.706

1.67

1.76

0.455

0.466

1.47

1.51

0.645

0.643

1.36

1.33

0.739

0.777

casein kinase II

L

16

0.75

0.58

0.538

0.358

0.76

0.58

0.535

0.330

0.90

0.60

0.493

0.322

0.97

0.61

0.454

0.309

ribonuclease

M

15

1.12

1.20

0.230

0.340

1.07

1.06

0.505

0.281

1.11

0.99

0.595

0.481

1.23

1.03

0.551

0.493

thermolysin

N

14

1.15

1.14

0.680

0.635

0.98

1.03

0.748

0.648

1.04

1.12

0.696

0.565

0.97

1.05

0.738

0.636

CDK2 kinase

O

13

1.06

0.80

0.841

0.812

1.14

1.01

0.733

0.817

1.14

1.02

0.729

0.661

1.12

1.14

0.640

0.525

glutamate receptor 2

P

13

1.08

0.85

0.070

0.096

1.09

0.85

0.120

0.097

1.08

0.85

0.116

0.121

1.00

0.84

0.123

0.016

P38 kinase

Q

13

0.55

0.57

0.834

0.896

0.76

0.66

0.762

0.757

0.95

0.62

0.799

0.764

0.59

0.51

0.870

0.896

β-secretase I

R

12

1.44

1.33

0.892

0.725

1.57

1.51

0.858

0.620

1.54

1.51

0.860

0.687

1.43

1.31

0.895

0.687

tRNA-guanine transglycosylase

S

12

0.90

0.95

0.463

0.544

1.06

1.04

0.212

0.375

0.87

0.95

0.457

0.403

0.87

0.95

0.457

0.522

endothiapepsin

T

11

1.18

1.30

0.435

0.215

1.28

1.35

0.358

0.210

1.35

1.36

0.345

0.215

1.36

1.27

0.480

0.210

α-mannosidase 2

U

10

1.67

1.63

-0.004

0.248

1.65

1.62

0.116

0.188

1.73

1.62

0.089

0.176

1.83

1.63

0.053

0.103

carboxypeptidase A

V

10

2.13

1.99

0.479

0.523

1.90

1.89

0.556

0.370

1.82

1.76

0.632

0.467

1.77

1.54

0.734

0.685

penicillopepsin

W

10

1.71

1.87

0.339

0.188

1.78

1.94

0.236

0.188

1.81

1.96

0.183

0.030

1.91

1.99

0.078

-0.030

families with 4-9 complexes

X

386

1.73

1.71

0.500

0.577

1.61

1.60

0.587

0.598

1.58

1.56

0.610

0.612

1.54

1.53

0.630

0.632

families with 2-3 complexes

Y

340

1.64

1.64

0.510

0.495

1.64

1.63

0.522

0.505

1.55

1.55

0.583

0.580

1.51

1.52

0.608

0.595

singletons

Z

321

1.76

1.74

0.407

0.417

1.81

1.75

0.397

0.395

1.70

1.68

0.476

0.467

1.67

1.65

0.503

0.507

average

  

1.35

1.24

0.493

0.470

1.38

1.27

0.465

0.414

1.37

1.23

0.515

0.450

1.33

1.18

0.545

0.479

standard deviation

  

0.41

0.38

0.216

0.217

0.38

0.37

0.209

0.212

0.39

0.36

0.211

0.211

0.39

0.35

0.228

0.251

Back to article page

BMC Bioinformatics

ISSN: 1471-2105

Contact us