SAMPLEX: Automatic mapping of perturbed and unperturbed regions of proteins and complexes

BMC Bioinformatics

Table 1 Performance of SAMPLEX

Subunit	CI2	BPN'	UBCH5	CNOT4	CE9	Im9	Average
SAMPLEX	0.72	0.62	0.51	0.76	0.46	0.47	0.59
Method A ¹	0.72	0.41	0.20	0.46	0.23	0.20	0.37
Method B ²	0.51	0.43	0.22	0.56	0.25	0.42	0.40

Comparison of the quality of the predictions for the interfaces of CI2, BPN', UBCH5, CNOT4, CE9 and IM9 using SAMPLEX and two commonly used methods as measured by the Matthews coefficient correlation (Eq. 8)
(1) Residues that have a CSP value higher than the average of all available CSP values plus one time their standard deviation are considered as perturbed
(2) Considering an iterative process, which consists on rejecting all residues with a CSP value higher than the average of all CSP values plus two times the standard deviation and starting again with remaining residues until no rejection occurs, all rejected residues are considered as perturbed.

ISSN: 1471-2105