ProtinDB - PROTein-protein INterface residues Data Base

Artificial Intelligence Research Laboratory

ProtInDb is a comprehensive database of protein-protein interface residues extracted from protein complexes in the Protein Data Bank (PDB).

This data base was built to satisfy two requirements:

  • Visualization of amino acid residues that belong to the interface between proteins chains.
  • Construction of data sets of protein-protein interface residues (IR) used to perform computational analyses and to train and test predictors of protein-protein interaction sites.

ProtInDb allows the user to compute interface residues using:

  • Three definitions of IR:
    • Based on the distances between the centers of the atoms in different protein chains.
    • Based on the distance between the Van der Waals surfaces of the atoms in partner chains.
    • Based on the distance between alpha carbon atoms in protein chains.
  • Interface residues are computed using a user-provided threshold value for each IR definition.
  • Surface residues can be determined by the user using a threshold value on the relative accesible surface area.
  • It is possible to compute the IR between a given chain and one or more partner chains in the complex.
  • IR can be computed from a given protein chain or from the protein chain and its sequence homologs (i.e. chains sharing >= 96% of sequence identity with the given chain).
  • IR can be extracted for the asymmetric units or the biological assemblies stored in PDB.

Datasets of protein-protein interface residues can be build from a list of protein chains provided by the user or from all the interacting proteins in ProtinDb. The selection of the final proteins in the dataset is supported by the stand alone program PISCES according to user-defined constrains on:

  • The maximum identity between the sequences of any pair of proteins in the final data set.
  • The resolution of the protein structures.
  • The R-value of the structures.
  • The lenght of the protein sequences.

The database is periodically updated to contain the set of non-deprecated interacting proteins in PDB. The date of the last update is shown at the bottom of the screens displaying results.


Last update of the data base from Protein Data Bank: 20160122.