Tracing conformational changes in proteins

BMC Structural Biology

Table 1 Performance statistics for the AdK, RBP, CVN and GroEL complex examples

	AdK	AdK RW^†	RBP	RBP RW^†	CVN	CVN RW^†	GroEL	GroEL RW^†
Initial lRMSD (Å)	6.95	6.95	4.06	4.06	16.01	16.01	14.64	14.64
#Residues	214	214	271	271	101	101	525^‡	525^‡
lRMSD after 1 hour (Å)	2.69±0.21	3.81±0.49	1.48±0.25	2.35±0.52	4.52±0.73	5.28±1.59	5.67±0.67	8.21±1.93
lRMSD after 2 hours (Å)	2.55±0.2	3.68±0.46	1.34±0.21	2.23±0.45	3.842±0.79	5.09±1.52	5.04±0.42	7.66±2.04
Final lRMSD (Å)	2.53±0.2	3.65±0.47	1.26±0.15	2.22±0.49	3.18±0.34	4.88±1.44	4.67±0.36	6.11±1.9

The average ± (standard deviation) lRMSD data were taken over 80 runs where the top and bottom 10% outliers were removed from the original set of 100 runs.
^† Random walk. See Results section for a discussion.
^‡ This is the number of residues per monomer. As explained in the text, the symmetry is exploited to model the entire 7-ring complex, which has 7 x 525 = 3675 residues.

ISSN: 1472-6807