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Table 3 Fragment clustering.

From: Fast structure similarity searches among protein models: efficient clustering of protein fragments

RMSD threshold (Å) N. struct. This work N N - 1 2 ratio Rep. Struct.
0.05 107,184 57,978,627 5,744,151,336 0.0100 79,994
0.1 79,994 28,610,140 3,199,480,021 0.0089 47,502
0.2 47,502 19,089,084 1,128,196,251 0.0169 13,066
0.4 13,066 4,479,481 85,353,645 0.0525 1,853
0.8 1,853 393,824 1,715,878 0.2295 131
Total 107,184 110,551,156 5,744,151,336 0.0193  
  1. Columns report the threshold RMSD chosen for clustering, the number of starting fragments, the number of RMSD computations done, the number of computations in an all-vs-all comparison, the number of representative fragments, used as starting fragments at the next iteration. CA atoms have been used for superposition.