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Table 1 Improvement of prediction quality due to atom specific weighting

From: Combination of scoring schemes for protein docking

  unopt amino acid specific atom specific amino acid × atom specific unopt amino acid specific atom specific amino acid × atom specific unopt amino acid specific atom specific amino acid × atom specific
Optimisation (Benchmark 2.0, 15°)
  Enzyme-Inhibitor (22) Antibody-Antigen (18) Others (30)
No on 1 0 1 3 3 0 1 1 1 0 0 0 0
No = 10 2 5 6 9 1 1 3 3 0 2 1 1
No = 50 4 12 13 14 1 3 6 5 1 4 5 5
No = 100 6 15 16 16 2 9 8 8 2 6 8 7
Average 1222 370 242 283 3119 462 267 295 3088 1560 1303 1323
Validation (Literature-data, 12°)
  Enzyme-Inhibitor (21) Antibody-Antigen (4) Others (4)
No on 1 1 1 1 4 0 0 0 0 1 0 0 0
No = 10 2 5 7 7 0 0 0 0 1 0 0 0
No = 50 6 10 14 12 1 0 0 0 1 0 0 0
No = 100 8 12 14 13 1 0 0 0 1 0 0 0
Average 918 720 669 606 9887 568 499 442 3493 5761 3513 4188
  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 a non-optimised ranking, based on the geometric correlation (unopt), a ranking based on the amino-acid specific weighting factors (amino acid specific), a ranking based on the atom specific weighting factors (atom specific), and for the combination of amino acid and atom specific ranking.