Skip to main content

Advertisement

Table 2 Combination of scoring schemes

From: Combination of scoring schemes for protein docking

  unopt amino acid × atom specific SVM AA × ATM & SVM unopt amino acid × atom specific SVM AA × ATM & SVM unopt amino acid × atom specific SVM AA × ATM & SVM
Validation (Literature-data, 12°)
  Enzyme-Inhibitor (21) Antibody-Antigen (4) Others (4)
No on 1 1 4 1 5 0 0 1 0 1 0 1 0
No = 10 2 7 7 13 0 0 1 0 1 0 1 0
No = 50 6 12 16 15 1 0 2 2 1 0 1 0
No = 100 8 13 18 17 1 0 2 2 1 0 1 0
Average 706 606 58 55 9887 442 299 115 3493 4188 1978 2701
Validation (Benchmark 2.0, 12°)
  Enzyme-Inhibitor (22) Antibody-Antigen (19) Others (29)
No on 1 0 2 4 3 0 1 0 1 0 0 0 1
No = 10 0 5 11 11 1 2 3 4 1 4 0 6
No = 50 1 12 18 19 1 3 7 10 2 7 5 7
No = 100 7 15 18 19 1 7 9 12 3 9 7 12
Average 897 416 113 104 5393 1245 350 302 4846 1219 1117 712
  1. Number of complexes for which a near-native structure can be predicted on the first and within the top10, top50 and top100 ranks. Furthermore the average rank of the first near-native structure is given. These quality measurements are shown for an non-optimised ranking, based on the geometric correlation (unopt), a ranking based on the combination of amino-acid specific and atom specific weighting factors (amino acid × atom specific), a ranking based on SVM scoring (SVM), and for the combination of amino acid, atom specific and SVM-based ranking AA × ATM & SVM. The combination of all three scoring schemes for enzyme-inhibitor complexes and for antibody-antigen complexes is done by ranking all structures by the SVM score and than ranking all structures with the same score again by the weighted geometric correlation. For the 'other' complexes the combination is done by multiplying all scores.