Secondary structure assignment reliability for DSSP, P-SEA and our program using randomly shifted PDB coordinates. The culled PDB set (described in methods) was used for this calculation. Gaussian random numbers were used to randomly shift coordinates of residues from 0.2Å to 2Å in steps of 0.2Å, in the PDB files. 100 files were generated for every file for every data-point leading to a total of 1,00,000 randomly shifted coordinate files. 2a: Mean and standard error of assignment consistency compared with assignment by the same program on the original coordinates. A percentage match was calculated by comparing definitions for the coordinate shifted file with the program output from actual file on a per residue basis. Means for the percentage match are shown. Standard errors were about 1% in each case (not shown). 2b: Average secondary structure content defined by each program for PDB files at different levels of perturbations are shown. The files used are the same as for fig. 8a. The number of residues assigned as helices or β-strands are shown as a percentage of total residues. Spaces and coils in the program output are counted for calculating percentages. 2c: Percentage of residues over-predicted by each program (DSSP, P-SEA, our method) with respect to the other two is shown. 100 files from the culled PDB set were used for these calculations. 35,670 residues were considered. Results shown are for over-predictions by program names in the column heads when compared with program names in the row heads. Actual number of helices and β-strands assigned by the program are shown on the diagonal (bracketed values).
Majumdar et al. BMC Bioinformatics 2005 6:202 doi:10.1186/1471-2105-6-202