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Table 1 Comparison of the efficacy of the programs

From: Efficient conformational sampling and weak scoring in docking programs? Strategy of the wisdom of crowds

Programs: sampling methods and scoring functions Conformational sampling Scoring
1-Number of poses obtained 2-Number of correct poses 3-Number of targets with a correct pose 4-Number of targets with a correct pose ranked in the top 4 5-Number of targets with a correct pose ranked as the top 1
FlexX 2915 910 65   
 FlexX     57 52
Surflex 2899 1152 84   
 Surflex     72 56
Glide-SP 2393 624 79   
 Glidescore     75 65
 Emodel     72 65
Glide-XP 392 210 74   
 Glidescore     73 68
 Emodel     73 66
Gold 1447 330 77   
 PLP     74 64
 Goldscore     73 60
USC based on docking results     87  
  1. The comparison is made for ligand conformational sampling (columns 1–3) and pose scoring (columns 4 and 5). From the requested 3000 poses per program (30 poses per target, for 100 targets), the number of obtained poses is given in the first column. Of these poses a certain number is correct, with RMSD < 2 Å from the crystal position, (column 2) and corresponding to a number of targets (column 3). The number of targets whose correct poses are ranked in the top 4 are given in column 4 and those whose correct poses are top-ranked are given in column 5. The number of targets with a correct pose obtained with the USC method, based on the docking results, is reported in the last line (see the “USC method” section below)