Docking protein domains in contact space

BMC Bioinformatics

Table 3 Data set of protein domains.

close conf		open conf		RMSD₁(Å)	RMSD₂(Å)	I_RMSD (Å)
1d4f	A1-A2	1b3r	A1-A2	0.76	0.45	0.67
1jmc	A1-A2	1fgu	A1-A2	1.47	2.18	0.93
1uae	O1-O2	1ejd	A1-A2	0.45	2.34	2.65
1a8e	O1-O2	1bp5	A1-A2	0.54	1.24	1.27
1arz	C1-C2	1dru	O1-O2	1.12	0.35	0.66
2dri	O1-O2	1urp	A1-A2	0.50	0.82	0.81
1tfb	O1-O2	1c9b	A1-A2	3.22	3.21	3.67
13pk	A1-A2	16pk	O1-O2	0.54	1.37	1.71
2nad	A1-A2	2nac	A1-A2	0.41	0.40	0.41
1ex7	A1-A2	1ex6	A1-A2	0.96	0.83	0.94
1tde	O1-O2	1f6m	E1-E2	0.68	1.03	0.71
9aat	A1-A2	lama	O1-O2	0.90	0.33	0.77
6adh	A1-A2	8adh	O1-O2	0.80	0.86	0.91
1h9m	A1-A2	1h9k	A1-A2	0.34	0.60	0.40
8atc	A1-A2	5atl	A1-A2	1.25	2.25	1.09
1l7p	A1-A2	1l7o	A1-A2	0.56	2.82	2.00
1njf	A1-A2	1njg	A1-A2	0.28	0.57	0.63
4cts	A1-A2	1cts	O1-O2	1.14	1.71	1.19
1dpp	A1-A3	1dpe	O1-O3	0.53	0.62	0.78
1dv2	A2-A3	1bnc	A2-A3	0.51	2.55	2.05

PDB codes and domain numbers (according to CATH) of the proteins in the close and open configurations. RMSD₁ and RMSD₂ are the C_α-RMSD respectively of domain 1 and 2 between the open and close configurations; I_RMSD is the C_α-RMSD of interface residues. The last two entries in the table are 3-domain proteins, all others are 2-domain proteins.

ISSN: 1471-2105