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Table 2 Results for the test systems

From: Systematic exploration of multiple drug binding sites

# Na CLSb #Rankc nd SRe
MDBSA MDF
1a 68 6 1 1 6 11
1bg 74 5 1 4 19
1cg 71 6 1 5 14
2 300 18 2 4 13 23
3a 222 46 3 4 21 11
3b 222 46 9 12 21 11
h 155 12 1 1 8 19
5 143 25 2 1 12 12
6i 116 26 1 2 12 10
7 123 26 4 4 12 10
8 106 25 1 1 10 11
9j 92 23 2 1 10 9
10 49 11 2 1 4 12
  1. aTotal count of ligand copies after Wrapper
  2. bCount of ligands surviving the Shaker, after MDBSA
  3. cRank serial number of the structure with the best RMSD value, after MDBSA and after MDF
  4. dCount of cluster representatives (final solutions) Shaker
  5. eShaker Rate
  6. fTotal computational time required for MDB, MDBSA and MDF, as explained in Additional file 2: Table S12
  7. gFor System 1, WnS was performed with different seeds for data reproduction purposes
  8. hFinal clustering was done using van der Waals and Coulomb interactions due to interactions of zinc ion with the ligand
  9. iWrapper process was done, using the LJ interaction as a scoring function, instead of AD4 (Additional file 2: Table S13)
  10. jFinal clustering was done with 6 Å distance limit between clusters