Table 1 The essential differences of DAPID, 3D-partner and 3D-interologs
Feature/Methods | DAPID [23] | 3D-partner [13] | 3D-interologs |
|---|---|---|---|
Homolog families of 3D- dimer template | NO | YES (BLASTP E-value <10-2) | YES (BLASTP E-value ≤10-10) |
Scoring function: | Â | Â | Â |
Template interface score | NO | NO | YES (E sηm ) |
Top ranked strategy | NO | NO | YES (Top ranked N for each species) |
Interface binding affinity | NO | YES (four matrices) | YES (four matrices) |
Residue conservation score | NO | YES (PSSM) | YES (PSSM) |
Score of aligned contact | Â | Â | Â |
residues | YES (BLOSUM62) | YES (BLOSUM62) | YES (BLOSUM62) |
Service type | A database of domain-annotated protein interactions | A web tool predicts interacting partners and binding models of a query protein sequence | An evolution database of physical protein-protein interactions across multiple genomes |