A generalized analysis of hydrophobic and loop clusters within globular protein sequences

BMC Structural Biology

Table 1 Frequencies of association of hydrophobic clusters with secondary structures: comparison of the different methods for secondary structure assignment.

α/β/C	Consensus	SSPDB	DSSP	STRIDE	PSEA
Consensus	1/1/1	0.99/0.99/0.98	0.99/0.99/0.99	0.99/0.99/0.92	0.99/0.99/0.99
SSPDB		1/1/1	0.99/0.99/0.98	0.99/0.98/0.91	0.99/0.99/0.99
DSSP			1/1/1	0.99/0.98/0.90	0.99/0.99/0.99
STRIDE				1/1/1	0.99/0.98/0.91
PSEA					1/1/1

Correlation coefficients were calculated with respect to the frequencies of association of the 294 hydrophobic cluster species reported in Additional file 3 with secondary structures (H, E, C; APC rule), following secondary structure assignment from different methods (SSPDB, DSSP, STRIDE, PSEA, consensus). The three values reported in the cells of this table correspond to the correlation coefficients calculated with respect to the different secondary structures (alpha, beta, coil).

ISSN: 1472-6807