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
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Interaction Type |
Evidence Type |
BioGRID |
The biological general repository for interaction datasets |
Direct and indirect |
- High throughput experiments
- Literature curation
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DIP |
Database of interacting proteins |
Direct |
- high throughput experiments
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DOMINE |
Database of protein domain interaction |
Direct |
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HPID |
Human protein interaction database |
Direct and indirect |
- PPIs Databases
- Prediction
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HPRD |
The human protein reference database. |
Direct |
- High throughput experiments
- Literature curation
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I2D |
Interolog interaction database |
Direct |
- PPIs databases
- Prediction
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iHOP |
Protein association network built by literature mining in PubMed |
Direct and indirect |
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IntAct |
Open source resource for molecular interaction data |
Direct |
- Literature curation
- User submissions
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MINT |
Molecular interaction database |
Direct |
- High throughput experiments
- Literature curation
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MIPS |
Mammalian protein-protein interaction database |
Direct |
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STRING |
Search tool for the retrieval of interacting genes/proteins |
Direct and indirect |
- Literature curation
- PPIs and pathway databases
- Predictions
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UniHI |
Unified human interactome |
Direct and indirect |
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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.
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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) |
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Interface Analysis
The following tools enable calculation of structural and chemical properties of macromolecular interfaces. Some of the calculated properties are listed here.
Ligplot |
Residue interactions (hydrogen bonds and hydrophobic interactions). Ligplot automatically generates schematic 2D diagrams of protein-ligand or protein-protein interactions. |
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LPC CSU |
Residues interactions (hydrophilic, hydrophobic, and aromatic interactions), contact surface area |
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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. |
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PIC |
Residue interactions (hydrogen and disulfide bonds, hydrophobic, ionic and aromatic
interactions) , accessible surface area |
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PISA |
Accessible surface area, buried surface area, solvation energy, residues interactions (hydrogen and disulfide bonds, salt bridges) |
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ProtoRP
| Accessible surface area, residues and atoms polarity, planarity, eccentricity, secondary structure info, residues interactions (hydrogen and disulfide bonds, salt bridges) |
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VASCo |
contact patch, hydrophobicity, electrostatic potential. VASCo includes PyMOL plugin to visualize annotated surfaces |
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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 |