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Table 1 Performance of four local methods deduced from an in silico testbed

From: H2rs: Deducing evolutionary and functionally important residue positions by means of an entropy and similarity based analysis of multiple sequence alignments

  Cut-off z-score Specificity Precision
  10-2 4.0 1.00 0.30
  10-2 2.0 0.97 0.18
  10-3 2.0 0.97 0.18
H2rs 10-4 2.0 0.98 0.19
  10-5 2.0 0.98 0.18
  10-10 2.0 0.98 0.17
  10-11 2.0 0.98 0.17
H2r    0.95 0.17
CMAT    0.77 0.13
SCA 0.7   0.53 0.12
1.5   0.84 0.15
3.0   0.99 0.15
  1. For all programs, specificity and precision were deduced from the analysis of 200 enzymes with known catalytic and binding sites. Residues with a maximal distance of 1 Å to a functional site were regarded as positives. All other residues were regarded as negatives. H2r and CMAT were used with default settings. For H2rs, the cut-off was applied to the p-value. For SCA, three cut-off values were chosen.