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Table 2 Performance of different COMBINE models a for the whole set of inhibitors in fitting and prediction

From: Exploring the binding of BACE-1 inhibitors using comparative binding energy analysis (COMBINE)

  

Data set 1b

Data set 2b

Electrostatic Modelsc

No. of PCs

r2

SDEC

q2

SDEP

r2

SDEC

q2

SDEP

1

1

0.709

0.78

0.653

0.948

0.588

0.929

0.51

1.153

 

2

0.82

0.614

0.713

0.914

0.793

0.659

0.701

0.816

 

3

0.871

0.521

0.74

1.131

0.891

0.477

0.703

1.074

 

4

0.917

0.417

0.713

0.989

0.91

0.435

0.761

1.096

 

5

0.944

0.344

0.691

1.00

0.923

0.402

0.775

0.98

2

1

0.252

1.336

0.149

1.609

0.295

1.215

0.106

1.571

 

2

0.718

0.994

0.528

1.116

0.78

0.679

0.704

0.913

 

3

0.856

0.848

0.657

0.931

0.824

0.607

0.719

0.785

 

4

0.898

0.805

0.691

1.097

0.896

0.466

0.747

1.06

 

5

0.921

0.824

0.677

1.131

0.92

0.41

0.786

0.988

3

1

0.212

1.37

0.105

1.623

0.26

1.245

0.045

1.621

 

2

0.773

0.845

0.66

0.85

0.79

0.663

0.725

0.949

 

3

0.864

0.819

0.68

1.088

0.819

0.617

0.731

0.796

 

4

0.922

0.889

0.623

1.007

0.897

0.465

0.728

0.728

 

5

0.956

1.002

0.521

0.87

0.916

0.419

0.772

0.816

  1. aAbbreviations: r2, correlation coefficient; SDEC, standard deviation of errors of correlation; q2, predictive correlation coefficient; SDEP, standard deviation of errors of prediction.
  2. bData set 1, all the BACE-1/inhibitor complexes were built from the A chain of 1 W51 and each of the co-crystallized ligands. All the co-crystallized ligands were translocated directly to the binding pocket of 1 W51 by a superimposition method using the Cα atoms (1 W51 structure as the reference), after this process, each BACE-1/inhibitor complex was energy minimized using the AMBER 9.0 program.
  3. Data set 2, all the BACE-1/inhibitor complexes were the actual complexes present in the PDB and energy minimized with the AMBER 9.0 program.
  4. cThe three types of electrostatic models. Model 1: a distance-dependent dielectric constant model. Model 2: a uniform dielectric constant model. Model 3: a sigmoidal model. The values in bold highlight the best quality models.