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Table 4 Fragment clustering on backbone.

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 53,793,796 5,744,151,336 0.0094 105,299
0.1 105,299 124,506,221 5,543,887,051 0.0225 87,195
0.2 87,195 57,001,567 3,801,440,415 0.0150 63,829
0.4 63,829 65,723,340 2,037,038,706 0.0322 21,637
0.8 21,637 33,375,313 234,069,066 0.1426 2,445
1.6 2,445 2,586,436 2,987,790 0.8657 33
3.2 33 528 528 1.0000 2
Total 107,184 336,987,202 5,744,151,336 0.0587  
  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. Atoms N, CA, C, O have been used for superposition.