Figure 6
From: SE: an algorithm for deriving sequence alignment from a pair of superimposed structures
Comparison of CPU times of SE and DP in SHEBA for one against all structure comparisons. Three proteins were selected, the smallest (1RYT http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd00350, 33 residues, in magenta), a medium sized (3AKY http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd01428, 204, orange) and the largest (1H18_A http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd01678, 747, green). Structure comparisons were made between each of these and all other 1164 domains using SHEBA with SE or DP. The average CPU time executed per DP cycle was divided by that per SE cycle for each pair and the ratio was plotted against the size of the target protein.