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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...

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-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 Organization

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....

Ligand Binding and Linkage

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...

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Related Experiment Video

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Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

A Point Cloud Graph Neural Network for Protein-Ligand Binding Site Prediction.

Yanpeng Zhao¹, Song He¹, Yuting Xing²

¹Academy of Military Medical Sciences, Beijing 100850, China.

International Journal of Molecular Sciences

|September 14, 2024

Summary

PGpocket, a geometric deep learning framework, enhances protein-ligand binding site prediction. This novel approach improves accuracy in drug design and understanding biological functions.

Keywords:

deep learning drug discovery graph neural network point cloud protein–ligand binding site structure representation

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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

Area of Science:

Structural Biology
Computational Chemistry
Drug Design

Background:

Accurate prediction of protein-ligand binding sites is crucial for drug discovery and understanding biological mechanisms.
Identifying these sites is a significant challenge in structural biology.
Existing methods often struggle with precision and efficiency.

Purpose of the Study:

To introduce PGpocket, a novel geometric deep learning framework.
To improve the accuracy and efficiency of protein-ligand binding site prediction.
To provide a practical tool for drug design and structural biology research.

Main Methods:

The PGpocket framework converts protein surfaces into point clouds.
Geometric and chemical properties of each point are calculated.
A graph neural network (GNN) is applied to a constructed point cloud graph for binding site prediction.

Main Results:

PGpocket achieved a 58% success rate on the Coach420 dataset.
PGpocket achieved a 56% success rate on the HOLO4K dataset.
Performance surpassed existing algorithms in independent tests.

Conclusions:

PGpocket demonstrates significant advancement in protein-ligand binding site prediction.
The framework offers a practical and accurate solution for drug design.
Geometric deep learning shows promise for complex biological predictions.