Systematic exploration of multiple drug binding sites

Table 2 Results for the test systems

#	N^a	CLS^b	#Rank^c		n^d	SR^e
#	N^a	CLS^b	MD_BSA	MD_F	n^d	SR^e
1a	68	6	1	1	6	11
1b^g	74	5	1	–	4	19
1c^g	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
4 ^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
9^j	92	23	2	1	10	9
10	49	11	2	1	4	12

^aTotal count of ligand copies after Wrapper
^bCount of ligands surviving the Shaker, after MD_BSA
^cRank serial number of the structure with the best RMSD value, after MD_BSA and after MD_F
^dCount of cluster representatives (final solutions) Shaker
^eShaker Rate
^fTotal computational time required for MD_B, MD_BSA and MD_F, as explained in Additional file 2: Table S12
^gFor System 1, WnS was performed with different seeds for data reproduction purposes
^hFinal clustering was done using van der Waals and Coulomb interactions due to interactions of zinc ion with the ligand
ⁱWrapper process was done, using the LJ interaction as a scoring function, instead of AD4 (Additional file 2: Table S13)
^jFinal clustering was done with 6 Å distance limit between clusters

ISSN: 1758-2946