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

Table 5 Comparing performance of side modelling methods

Method	RMSD (Å)			Contact score	χ₁(± 15°)	χ₁₊₂(± 15°)
	All	Buried	Exposed		%	%
Hunter	1.47	0.73	1.72	39	79	60
OPUS-Rota [26]	1.56	0.91	1.80	35	77	56
SCAP [50]	1.72	1.00	1.96	37	69	46
SCCOMP [42]	1.72	1.03	1.96	34	69	49
SCWRL4.0 [51]	1.65	0.87	1.93	35	76	55

Side chains were rebuilt using five different methods in a set of 94 high-resolution protein structures. The average statistics on side chain prediction accuracy was calculated in terms of side chain RMSD, contact score, and chi-angle prediction accuracy. Side chain RMSD was calculated for side chain atoms except Cβ. A residue was considered as exposed or buried if its relative solvent exposed area is greater or less than 15%, respectively. Contact score reflects amount of correctly predicted atom-atom contacts and is calculated as described in Methods.