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Table 3 Comparison of the conservation information provided by WildSpan with that of MSA

From: WildSpan: mining structured motifs from protein sequences

 

Total number of residues characterized as conserved

Number of interface residues in the group of residues categorized as conserved

Proportion of interface residues in the group of residues categorized as conserved

W-patterns

10268

2351

23.6%

MSA

10638

2058

18.7%

  1. We investigated the property of W-patterns at residue level by calculating the proportion of interface residues in W-patterns. The results are compared with the conserved residues assigned by Clustal-W (MSA). The experiments were tested on the 217 of 220 protein chains (PP220) in the protein-protein benchmark (no homologues can be found for the three cases: 1ml0_A, 1ml0_B, 1udi_I).
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Algorithms for Molecular Biology

ISSN: 1748-7188