| COMPARISON MATRICES |
| |
| |
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:
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:
A value of ci greater than 1 indicates a conservation of the binding pocket amino acids stronger than the rest of the protein.
|
