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Protein-protein Interfaces

Protein-protein Interfaces

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...

Protein Networks

Protein Networks

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,...

Protein-Protein Interfaces

Protein-Protein Interfaces

Ligand Binding Sites

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

Protein Complex Assembly

Protein Complex Assembly

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Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

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Published on: November 17, 2019

OpenPIP: An Open-source Platform for Hosting, Visualizing and Analyzing Protein Interaction Data.

Mohamed Helmy¹, Miles Mee², Aniket Ranjan³

¹Department of Computer Science, Lakehead University, Thunder Bay, ON, Canada.

Journal of Molecular Biology

|June 6, 2022

Summary

This summary is machine-generated.

Researchers developed the Open-source Protein Interaction Platform (openPIP), a customizable web portal for storing and visualizing protein-protein interaction (PPI) data. This free tool simplifies sharing experimental interactome maps without requiring coding skills.

Keywords:

interactome protein interaction database protein interactions

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Area of Science:

Proteomics
Bioinformatics
Computational Biology

Background:

Understanding protein-protein interactions (PPIs) is crucial for deciphering cellular processes and disease mechanisms.
Advances in high-throughput technologies have generated extensive genome-wide PPI maps.
Disseminating and analyzing these complex datasets presents a significant challenge.

Purpose of the Study:

To develop a user-friendly, customizable web portal for hosting and sharing experimental PPI maps.
To provide a solution for researchers to store, visualize, and analyze PPI data without requiring coding expertise.
To facilitate the dissemination of interactome data alongside primary research publications.

Main Methods:

Development of the Open-source Protein Interaction Platform (openPIP) as a web-based portal.
openPIP is designed as a customizable solution requiring no coding skills for setup and customization.
The platform is available as a ready-to-use Docker container for easy deployment.

Main Results:

openPIP enables the storage, visualization, analysis, and web-based dissemination of experimental PPI maps.
The platform has been successfully utilized to create web portals for the Human and Yeast Reference Protein Interactome maps (HuRI and YeRI).
openPIP offers a no-code solution for researchers to manage and share their PPI datasets.

Conclusions:

openPIP provides a valuable, accessible resource for the scientific community to manage and share protein-protein interaction data.
The platform streamlines the process of making complex interactome datasets publicly available.
openPIP supports the broader goals of data sharing and reproducibility in biological research.