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  Sequence identity of the PDB entries
For each pair [a,b] of protein structures in complex with a selected ligand, the amino acid conservation c[a,b] of the binding pocket is defined as the average value of the conservation c[a/b] of a with respect to b (deduced from the FASTA pair wise alignment with b as query the sequence) and that of c[b/a]; the value of c[a/b] being defined as:

c[a/b] = Number of conserved binding pocket residues of a with respect to b
Number of binding pocket residues of b
If one of the two pair wise alignments is not present or not reliable (e.g., in the case the FASTA Expectation Value is greater than 10-3 for the pair [a,b] but not for the pair [b,a]), the value of c[a/b] is assumed also by c[b/a]. If the Expectation Value is grater than threshold 10-3 in both the alignment of a with respect to b and in that of b versus a, the corresponding value in the matrix is set to 0.
  Overall amino acid conservation
This matrix represents the percent sequence identity between pair of proteins. Pair of sequences having an Expectation Value above 10-3 have been assigned the conventional value 0.
  Ratio between conservation of binding pocket residues and overall sequence conservation
Indicating with si[a,b] the sequence identity between a and b, a further measure of the binding pocket similarity is provided by the conservation index ci[a,b], defined as:

ci[a,b] = c[a,b]
A value of ci greater than 1 indicates a conservation of the binding pocket amino acids stronger than the rest of the protein.