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

BMC Structural Biology

Table 2 Propensities of hydrophobic clusters for secondary structures: comparison of the different methods for secondary structure assignment.

α/β/C/M	SSPDB	STRIDE	DSSP	PSEA	Consensus
SSPDB	1/1/1/1	0.99/0.93/0.97/0.83	0.99/0.94/0.98/0.86	0.97/0.92/0.79/0.77	0.99/0.94/0.98/0.86
STRIDE		1/1/1/1	0.99/0.99/0.98/0.97	0.97/0.95/0.80/0.79	0.99/0.99/0.98/0.97
DSSP			1/1/1/1	0.97/0.94/0.79/0.78	0.99/0.99/0.99/0.99
PSEA				1/1/1/1	0.97/0.95/0.79/0.79
Consensus					1/1/1/1

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

ISSN: 1472-6807