Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions

BMC Bioinformatics

Table 1 Performance of the ScSc knowledge-based term in modelling

Atom set	Histogram type	Bin size, Å	Side chain RMSD, Å
			Reduced RL	Full RL
Atom Set 1	Smoothed	0.25	2.37	2.95
		0.50	2.28	2.89
		0.75	2.41	3.00
		1.00	2.47	3.04
	Non-smoothed	0.25	2.69	3.32
		0.50	2.58	3.21
		0.75	2.55	3.08
		1.00	2.46	3.04
Atom Set 2	Smoothed	0.25	2.42	3.11
		0.50	2.38	3.03
		0.75	2.43	3.16
		1.00	2.53	3.17
	Non-smoothed	0.25	2.67	3.47
		0.50	2.62	3.27
		0.75	2.53	3.14
		1.00	2.43	3.06

To determine the best combination of parameters for the ScSc term, a set of 30 proteins was remodelled using the ScSc term only with different atom sets, bin sizes, and with or without histogram smoothing. The side chain RMSD was calculated for side chains atoms excluding Cβ atoms. Results for both the reduced and full rotamer libraries are presented.

ISSN: 1471-2105