Binary image representation of a ligand binding site: its application to efficient sampling of a conformational ensemble

Table 1 Statistics on bit string generation for MMP-1 and MMP-13 ligand binding pockets.

Item	MMP-1	MMP-13 full	MMP-13D	MMP-13P
# of FLRs¹	23	27	23	13
# of SLRs²	13	21	13	8
# of CCRs³	11	19	11	5
# of all 3D points	809	1,222	614	621
# of points free of contacts	578	740	223	507
# of conditional contact points	231	482	391	114
# of all conformers free of bumping	362,862	71,066,419,200	6,326,207	1,380
# of non-redundant bit strings	8,000	-	358,752	143
# of unique strings after merge⁴	-	-	33,172	-
Reduction in 'computational complexity'⁵ (f old)	41	-	190.7	9.58
Run time for two-way clustering (Cluster 3.0)⁶	9min		370 min	<1 sec

¹The residues within 5 Å from the ligand ensemble
²The residues within 3 Å from the 3D points that are within 1 Å from FLRs
³The residues showing 'conditional' contacts with the 3D points
⁴Bit strings differ by less than 5 bits were merged
⁵The ratio defined as [# of all conformers free of bumping]/[# of non-redundant bit strings]
⁶CPU time elapsed using an Intel Xeon E5430 CPU operating at 2.66 GHz with 24 GB of main memory (the maximum virtual memory usage was 4.4 GB) on a linux box.

ISSN: 1471-2105