N-BIO BINDS

Predict domain-domain interface

PreDom:Interface predicts domain-domain interaction residues from the 3D structure of domain. Domain interface residues are predicted by two algorithm; KIP and IP.

  • KIP (Known Interface residue Positions): Domain interface residues are predicted using the positions of known domain interface residues in homologous domains(in SCOP or CATH).
  • IP (Interface Propensity): Domain interface residues are predicted using the prediction score calculated from interface propensity, which means usage preference in domain-domain interfaces compared to the other part of domain surface. To increase the specificity of prediction, two interface propensities, "core" and "peripheral", are used for the score calculation.

Database SCOP CATH
Input
PDB format file: chain:
Parameters
KIP method Threshold of sequence identity: % Threshold of sequence coverage: % Threshold of BLAST E-value:
IP method Threshold of IP score: Threshold of residue contact: Å Minimum size of interface: aa.

Sample PDB file