Discriminating the native structure from decoys using scoring functions based on the residue packing in globular proteins

Table 6 R_s and R_p for two proteins having the same fold belonging to the β class

Name of the protein	Number of residues	Number of aligned residues	R_s	R_p
Azurin (1azu)	126	84	1.12 (1.06)	0.33 (0.29)
Plastocyanin (5pcy)	99	84	1.33 (1.14)	0.46 (0.32)

The structures are aligned using the software SSM at EBI http://www.ebi.ac.uk/msd-srv/ssm. The values calculated considering only the aligned amino acid residues are given in parenthesis. To quantify the sequence structure compatibility between the structures, two more parameters are computed over the aligned residues. (R_s)_azu/pcy = 0.97 and (R_s)_pcy/azu = 0.89. Each term contributing to the former corresponds to (ASA_azu - <ASA>_pcy)/<ASA>_pcy, i.e., in Eq. (3) the observed value at a given position in the structure of azurin is compared to the average value corresponding to the aligned residue type at the same position in the sequence of plastocyanin. The opposite is done in the calculation of (R_s)_pcy/azu.

ISSN: 1472-6807