Find protein interactions to your protein sequence of interest.
Until a sequence has a known three dimensional structure (probably as part of a complex), we do not definitively know that an interaction exists. The search service we provide identifies any protein domains in the query sequence, then for each found domain, looks in the iPfam catalogue for previously observed interacting partners. We do not provide any metric of confidence regarding the predictions and users should treat the predictions as that, a prediction
The database serves as a resource for researchers aiming to understand protein interactions at the domain level, facilitating the study of how proteins interact within cellular networks. It has been utilized in various studies to analyze the reuse of structural domain–domain interactions across different species, highlighting the conservation and modularity of these interactions in protein networks.
iPfam's data is particularly useful for predicting potential interactions in proteins lacking experimental interaction data, as it allows for the inference of interactions based on known domain relationships. This predictive capability aids in the exploration of protein functions and the mapping of interaction networks, contributing to advancements in fields such as structural biology and bioinformatics.
Proteins are the building blocks of life, and their interactions form the foundation of countless biological processes. Understanding these interactions is crucial for unraveling the complexities of cellular mechanisms and advancing fields such as medicine, biotechnology, and structural biology.
Explore the World of Protein Interactions
Our platform is dedicated to providing comprehensive resources and tools for studying protein interactions. Whether you're a researcher, student, or enthusiast, you'll find valuable information to deepen your understanding of:
Protein-Protein Interactions (PPIs):
Uncover how proteins communicate and collaborate within cellular networks.
Ligand Binding:
Discover how small molecules interact with proteins, revealing potential therapeutic targets.
Protein-Domain Interactions:
Delve into the modular structures that drive protein functions and interactions.
Why Study Protein Interactions?
Protein interactions are at the heart of everything from immune responses to metabolic pathways. By understanding these connections, scientists can:
- Develop new drugs by targeting specific interactions.
- Investigate the molecular basis of diseases.
- Engineer proteins with novel functions.
Biological Techniques Used to Study Protein Interactions
Biochemical Techniques
- Co-immunoprecipitation (Co-IP): Detects physical interactions by using specific antibodies to isolate a protein and its binding partners from a mixture.
- Pull-Down Assays: Uses a tagged "bait" protein to isolate and identify interacting proteins ("prey").
- Affinity Chromatography: Separates and purifies proteins based on their specific binding to an immobilized ligand.
- Western Blotting (WB): Often combined with Co-IP to confirm the presence of interacting proteins using specific antibodies.
Biophysical Techniques
- Surface Plasmon Resonance (SPR): Measures real-time interactions and binding affinities between proteins or protein-ligand pairs.
- Isothermal Titration Calorimetry (ITC): Evaluates thermodynamic parameters (e.g., binding constants, enthalpy changes) of interactions.
- X-ray Crystallography: Determines the atomic-level structure of protein complexes to reveal interaction interfaces.
- Nuclear Magnetic Resonance (NMR) Spectroscopy: Identifies protein interaction sites in solution and provides insights into binding dynamics.
- Cryo-Electron Microscopy (Cryo-EM): Captures high-resolution images of large protein complexes to understand their interactions.
Genetic and Molecular Biology Techniques
- Yeast Two-Hybrid (Y2H): A genetic system used to detect and study binary protein-protein interactions within yeast cells.
- Split-GFP or Split-Luciferase Assays: Reconstructs functional fluorescent or luminescent proteins when two interacting proteins are close.
- CRISPR-Cas9 Screening: Identifies genes involved in protein interaction pathways by knocking out or modifying target genes.
- Phage Display: Displays peptide or protein fragments on phage surfaces to study binding interactions.
High-Throughput Techniques
- Mass Spectrometry (MS)-Based Proteomics: Identifies proteins co-purified in complexes, providing insights into large interaction networks.
- Protein Microarrays: Screens thousands of proteins for binding partners or functional interactions in a high-throughput manner.
- Proximity-Dependent Labeling (e.g., BioID, APEX): Tags interacting proteins in living cells for identification via mass spectrometry.
Cellular and Microscopy Techniques
- Fluorescence Resonance Energy Transfer (FRET): Detects protein interactions by measuring energy transfer between fluorophores on interacting proteins.
- Bimolecular Fluorescence Complementation (BiFC): Visualizes protein interactions in live cells using fluorescent protein fragments that assemble upon interaction.
- Confocal Microscopy: Tracks the localization and dynamics of interacting proteins in cells with high spatial resolution.
- Proximity Ligation Assay (PLA): Detects close interactions between two proteins in situ using antibody-based techniques.
Computational and In Silico Techniques
- Molecular Docking: Predicts how proteins interact based on their 3D structures.
- Protein Interaction Networks (PINs): Maps and analyzes interaction networks to reveal functional relationships between proteins.
- Molecular Dynamics (MD) Simulations: Simulates protein interactions and explores their stability and dynamics over time.