Related Experiment Video
Updated: Sep 20, 2025
13:56
A Comparative Approach to Characterize the Landscape of Host-Pathogen Protein-Protein Interactions
Published on: July 18, 2013
11.3K
HPiP: an R/Bioconductor package for predicting host-pathogen protein-protein interactions from protein sequences
Matineh Rahmatbakhsh1, Mohamed Taha Moutaoufik1, Alla Gagarinova2
1Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada.
Bioinformatics Advances
|June 7, 2022
Summary
HPiP software predicts host-pathogen protein-protein interactions (PPIs) using machine learning. This tool aids in understanding infections and identifying drug targets for pathogens like SARS-CoV-2 and Mycobacterium tuberculosis.
Area of Science:
- Computational biology
- Infectious disease research
- Bioinformatics
Background:
- Experimental identification of host-pathogen protein-protein interactions (PPIs) is challenging and time-consuming.
- Understanding these interactions is crucial for deciphering infection mechanisms and discovering therapeutic targets.
Purpose of the Study:
- To develop a computational tool for predicting host-pathogen PPIs.
- To accelerate the study of under-explored pathogens and identify potential drug targets.
Main Methods:
- Developed HPiP (Host-Pathogen Interaction Prediction), an R/Bioconductor package.
- Utilized amino acid sequence property descriptors and ensemble machine learning classifiers.
- Trained and tested models using SARS-CoV-1, SARS-CoV-2, and Mycobacterium tuberculosis-human PPI data.
Main Results:
- HPiP demonstrated strong performance in predicting SARS-CoV-2-human PPIs, validated experimentally.
- The software accurately predicted known PPIs for Mycobacterium tuberculosis and human proteins.
- HPiP provides a valuable resource for systems-level understanding of host-pathogen interactions.
Conclusions:
- HPiP software effectively predicts host-pathogen PPIs, facilitating research on infectious diseases.
- The tool aids in identifying novel therapeutic targets and repurposing existing drugs.
- HPiP is openly available, promoting broader scientific exploration.
Related Concept Videos
02:04Protein-protein Interfaces
13.8K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
13.8K
02:26Protein Networks
4.1K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.1K