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Table 6 Filtering cutoffs for removing redundancy in the testing sets.

From: The AnnoLite and AnnoLyze programs for comparative annotation of protein structures

 

Initial set

Sequence Identity (%)

Equivalent positions (%)

RMSD (Å)

Difference in length

Final set

Annotation

10,997

N/A

≥60.0

≤2.0

≤30

1,879

Ligand

30,126

≥30.0

≥75.0

≤4.0

≤50

4,948

Partner

30,425

≥30.0

≥75.0

≤4.0

≤50

4,613

Localize

30,126

≥90.0

≥90.0

≤2.0

N/A

1,936

  1. Sequence identity is the percentage of identical residues with respect to the aligned positions in the structural alignment. Equivalent position is the percentage of residues that align within 4 Å with respect to the shorter of the two aligned structures. The RMSD is calculated using Cα atoms of the two aligned structures.