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.
Interaction Type ![]() |
Evidence Type ![]() |
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BioGRID | The biological general repository for interaction datasets | Direct and indirect |
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DIP | Database of interacting proteins | Direct |
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DOMINE | Database of protein domain interaction | Direct |
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HPID | Human protein interaction database | Direct and indirect |
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HPRD | The human protein reference database. | Direct |
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I2D | Interolog interaction database | Direct |
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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 |
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MINT | Molecular interaction database | Direct |
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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 |
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UniHI | Unified human interactome | Direct and indirect |
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Interface criteria | ||
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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) |
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) |
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 | |
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 |
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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 | |
I2I-SiteEngine | Structural and physico-chemical alignment of protein-protein interfaces | |
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MAPPIS | Multiple alignment of protein-protein interfaces | |
webPIPSA | Comparison of the electrostatic interaction properties of proteins |