. Author manuscript; available in PMC: 2011 May 18.

Published in final edited form as: Biochemistry. 2010 May 18;49(19):4283–4295. doi: 10.1021/bi100569u

Table 4.

Variations in the number of efficient communications established with the active site with respect to apo simulations (reference distance: 15 Å). The number of new and lost communications is reported in parenthesis.

Ligand	ΔComm (BLAI)	ΔComm (BV6)	ΔComm (BMDR)
INDINAVIR	+30 (38 / 8)	+8 (19 / 11)	-24 (6 / 30)
NELFINAVIR	+28 (36 / 8)	-19 (0 / 19)	+ 10 (26 / 16)
RITRONAVIR	+37 (43 / 6)	-8 (2 / 10)	-16 (12 / 28)
TL-3	+48 (51 / 3)	+9 (15 / 6)	+2 (21 / 19)
SUBSTRATE	+17 (27 / 10)	+26 (32 / 6)	-9 (8 / 17)
SUBSTRATE ^(*)	//	//	0 (13 / 13)
SUBSTRATE ^(**)	//	//	+ 8 (18 / 10)

^(*)

The BMDR value has been calculated on the last 10 ns of the original MD simulation.

^(**)

The BMDR value has been calculated on the 20 ns extension of the MD simulation.