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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-Protein Interfaces

Protein-Protein Interfaces

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

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,...

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 Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...

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A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Highly precise protein-protein interaction prediction based on consensus between template-based and de novo docking

Masahito Ohue, Yuri Matsuzaki, Takehiro Shimoda

BMC Proceedings

|February 26, 2014

Summary

A new computational method improves protein-protein interaction (PPI) prediction precision by combining template-based and de novo docking approaches. This enhanced accuracy in predicting PPI networks can reduce experimental validation costs and aid interactome analysis.

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A Protocol for Computer-Based Protein Structure and Function Prediction

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Area of Science:

Computational biology
Network biology
Drug discovery

Background:

Protein-protein interaction (PPI) networks are crucial for understanding diseases and developing drugs.
Current in silico PPI prediction methods (template-based and de novo docking) have limitations in applicable range, prediction performance, and precision.
Existing methods require costly experimental validation for predicted PPIs, necessitating more precise prediction tools.

Purpose of the Study:

To develop a novel structure-based method for predicting protein-protein interactions (PPIs).
To enhance the precision of in silico PPI prediction compared to existing methods.
To reduce the expenditure associated with experimental validation of predicted PPIs.

Main Methods:

A hybrid approach combining template-based and de novo docking prediction strategies was developed.
The method utilizes tertiary-structure information for PPI prediction.
The approach was applied to predict the human apoptosis signaling pathway network.

Main Results:

The proposed consensus method achieved a precision of 0.333 for PPI prediction in the human apoptosis signaling pathway.
This precision is significantly higher than conventional methods like PRISM (0.231) and MEGADOCK (0.145).
The method maintained a comparable F-measure (0.285) to conventional methods (PRISM: 0.296, MEGADOCK: 0.220).

Conclusions:

The consensus method demonstrates superior precision in predicting PPI networks compared to existing template-based and non-template-based methods.
This increased precision has the potential to decrease the cost and effort of laboratory validation for novel PPIs.
The developed method can serve as a valuable tool to facilitate and advance interactome analysis.