Protein-Protein Interactions

Protein-protein interactions (PPIs) represent a key feature of protein function. Almost every cellular process relies interaction of two or more proteins in order to accomplish a particular task. The following web utilities, databases and programs can help you in finding and analyzing interactions between proteins.

Protein-Protein Interaction Databases

    Interaction Type Read More Info Evidence Type Read More Info
BioGRID The biological general repository for interaction datasets Direct and indirect
  • High throughput experiments
  • Literature curation
DIP Database of interacting proteins Direct
  • high throughput experiments
DOMINE Database of protein domain interaction Direct
  • PDB
  • Prediction
HPID Human protein interaction database Direct and indirect
  • PPIs Databases
  • Prediction
HPRD The human protein reference database. Direct
  • High throughput experiments
  • Literature curation
I2D Interolog interaction database Direct
  • PPIs databases
  • Prediction
iHOP Protein association network built by literature mining in PubMed Direct and indirect
  • User literature curation
IntAct Open source resource for molecular interaction data Direct
  • Literature curation
  • User submissions
MINT Molecular interaction database Direct
  • High throughput experiments
  • Literature curation
MIPS Mammalian protein-protein interaction database Direct
  • Literature curation
STRING Search tool for the retrieval of interacting genes/proteins Direct and indirect
  • Literature curation
  • PPIs and pathway databases
  • Predictions
UniHI Unified human interactome Direct and indirect
  • PPIs databases

Protein-Protein Interface Databases

An interface can be defined as the set of amino acids which represents a region that links two polypeptide chains in a protein structure by non-covalent interactions. The following databases include protein-protein interfaces extracted from experimentally determined structures of protein complexes in the PDB.

    Interface criteria
PIBASE A database of structurally defined protein interfaces Distance ( ≤ 6.05 Å) - include water mediated contacts
PPIDB Protein-Protein Interface Database Distance, ASA (user defined thresholds)
PRINT Dataset of protein protein interfaces Distance (≤ 5.0 Å)
SCOPPI Structural classification of protein-protein interfaces Distance (≤ 5.0 Å)
SCOWLP Structural Characterization Of Water, Ligands and Proteins Distance ( ≤ 9.0 Å) - include water mediated contacts
SNAPPI Structures, interfaces and alignments for protein-protein interactions Distance ( ≤ sum of van der Waals radii + 0.5 Å for atom pair )
3DID 3D interacting domains No. of interactions ( ≥ 5 hydrogen bonds/salt bridges/VDW interactions)

Interface Analysis

The following tools enable calculation of structural and chemical properties of macromolecular interfaces. Some of the calculated properties are listed here.
Residue interactions (hydrogen bonds and hydrophobic interactions). Ligplot automatically generates schematic 2D diagrams of protein-ligand or protein-protein interactions.
Read more Info
LPC CSU Residues interactions (hydrophilic, hydrophobic, and aromatic interactions), contact surface area  
MolSurfer Complementarity, hydrophobicity and electrostatic potential. MolSurfer is a graphical tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures.  
PIC Residue interactions (hydrogen and disulfide bonds, hydrophobic, ionic and aromatic
interactions) , accessible surface area
PISA Accessible surface area, buried surface area, solvation energy, residues interactions (hydrogen and disulfide bonds, salt bridges)  
ProtoRP Accessible surface area, residues and atoms polarity, planarity, eccentricity, secondary structure info, residues interactions (hydrogen and disulfide bonds, salt bridges)  
VASCo contact patch, hydrophobicity, electrostatic potential. VASCo includes PyMOL plugin to visualize annotated surfaces  

Interface Comparison

I2I-SiteEngine Structural and physico-chemical alignment of protein-protein interfaces
MAPPIS Multiple alignment of protein-protein interfaces
webPIPSA Comparison of the electrostatic interaction properties of proteins