Table 2

Performance of different COMBINE modelsafor the whole set of inhibitors in fitting and prediction
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

aAbbreviations: r2, correlation coefficient; SDEC, standard deviation of errors of correlation; q2, predictive correlation coefficient; SDEP, standard deviation of errors of prediction.

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.

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.

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.

Liu et al.

Liu et al. BMC Structural Biology 2012 12:21   doi:10.1186/1472-6807-12-21

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