Improved protein structure selection using decoy-dependent discriminatory functions

BMC Structural Biology

Table 1 Correlation coefficients between C_α RMSDs of decoys relative to the experimentally determined conformations and scores generated by the density score function, the self-RAPDF and other published scoring functions applied to the 4state_reduced decoy sets.

Protein (PDB code)	Number of conformations	Empirical function [32]	Atomic KBP [8]	Shell [33]	RAPDF [7]	Density score	Self-RAPDF
1ctf	630	0.68	0.6	0.65	0.73	0.98	0.89
1r69	675	0.66	0.5	0.52	0.70	0.96	0.88
1sn3	660	0.53	0.5	0.42	0.47	0.96	0.89
2cro	674	0.58	0.7	0.58	0.76	0.96	0.92
3icb	653	0.77	0.8	0.74	0.85	0.98	0.92
4pti	687	0.46	0.5	0.34	0.49	0.95	0.89
4rxn	677	0.61	0.6	0.57	0.57	0.98	0.88

The density scores and the self-RAPDF scores have the best correlation coefficient with C_α RMSDs of decoys relative to experimentally determined conformations for all seven sets.

ISSN: 1472-6807