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Table 3 Comparison of three TNF-α and 122 HIV-1 RT non-nucleoside binding sites by state-of-the-art cavity comparison methods

From: Unexpected similarity between HIV-1 reverse transcriptase and tumor necrosis factor binding sites revealed by computer vision

Method Score thresholda Metric Success rateb
G-LoSA 0.59 GA-score 35.2
KRIPO 0.50 Modified Tanimoto coefficient 5.8
Shaper 0.44 ColorRefTversky 1.4
SiteAlign 0.6, 0.2 d1 and d2 distancesc 0.3
FuzCav 0.16 Tanimoto coefficient 0
ProBiS 2 Z-scored 0
ProCare 0.47 ProCare score 76.6
  1. aDeveloper’s recommended similarity/distance threshold for estimating two binding sites similar
  2. bPercentage of pairwise comparisons scored above the threshold
  3. cFor SiteAlign comparisons, pairs are considered similar when the two distances (d1, d2) are below the score threshold value [37]
  4. dThe Z-score indicates the statistical relevance of ProBiS binding site alignments