Where the sum runs for all the distance bins.
There are 15 distance bins covering the range from 0 to 60 A. di
is the distance representing each bin, its upper limit (normalised to
60). Pip is the percentage of predicted pairs whose distance is
included in the i bin. Pia
is the same for all the pairs. Defined in that way, Xd>0 indicates
the positive cases where the population of predicted contacts distances
is shifted to lower distances (see J. Mol. Biol. (1997), 271:511-523).
For the calculation of these parameters, both,
the predicted pairs of residues and all the pairs in the protein are
split in three sets according to the separation of the two residues of
the pair in the linear sequence of the protein, the number of residues
between them: seqsep>=6, seqsep>=12 and seqsep>=24. Acc, Imp,
Cov and Xd are evaluated for these three sets.
The main
parameter for the evaluation is the highest sequence separation
(seqsep>=24).
The list of the predicted contacts is sorted by the assigned score and
evaluations are made taken
different numbers of top pairs as function of the protein length: the
first L/10, L/5, L/2, L and 2L pairs are taken (L or Len: number of
residues of the protein). For 3D prediction servers that do not have
values of reliability
associated to each pairwise distance, we sample an equivalent number of
predicted pairs. All those calculations are performed for the three
subsets of
pairs (seqsep>=6, 12 and 24).
