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Introduction of Some Parameters


  • PPS-score
    In order to measure the alignment accuracy, we define a scoring function, PPS-score, as follows:

    PPS-score = 2 ∑Lali1/(1 + (di/d0)2) / (LQ+LT)

    where Lali and di are the residue number of the aligned pairs and the distance between the Ca atoms of the i-th pair of the aligned pairs, respectively. d0 is the corresponding scale to normalize the corresponding match difference. d0 = 0.45 * ((LQ+LT)/2-7)1/2 + 0.55. LQ and LT are the residue numbers of query (Q) and template pockets. In PPS-align, we will search the maximum of PPS-score for each pocket pair.
  • Jaccard Ratio
    Let LQ, LT and Lali be the residue numbers of query pocket, template pocket, and the aligned pairs, respectively. The equation of Jaccard Ratio as follows:
    Jaccard Ratio = Lali / (LQ + LT - Lali).

    See also : Jaccard Index.
  • Alignment Information
    • 'Query AA Index' means the orginal residue indexes of the inputted query pocket.
    • 'Templ AA Index' means the orginal residue indexes of the inputted templ pocket.

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