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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...

Ligand Binding Sites

Ligand Binding Sites

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...

Conserved Binding Sites

Conserved Binding Sites

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...

Ligand Binding and Linkage

Ligand Binding and Linkage

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Simple Ligand-Receptor Interaction Descriptor (SILIRID) for alignment-free binding site comparison.

Vladimir Chupakhin¹, Gilles Marcou¹, Helena Gaspar¹

¹Laboratory of Chémoinformatics, UMR 7140, University of Strasbourg, France.

Computational and Structural Biotechnology Journal

|September 12, 2014

Summary

We introduce SILIRID (Simple Ligand-Receptor Interaction Descriptor), a new method to describe protein-ligand interactions. This descriptor efficiently distinguishes protein binding sites and visualizes chemical genomics data.

Keywords:

Chemogenomics Generative Topographic Mapping Interaction fingerprints Protein classification Protein similarity Protein–ligand interactions

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Area of Science:

Computational biology
Structural biology
Cheminformatics

Background:

Protein-ligand interactions are crucial for biological processes and drug discovery.
Existing methods for characterizing these interactions can be complex and computationally intensive.
A need exists for efficient and informative descriptors of protein-ligand binding sites.

Purpose of the Study:

To introduce SILIRID (Simple Ligand-Receptor Interaction Descriptor), a novel fixed-size descriptor for protein-ligand interactions.
To evaluate SILIRID's performance in distinguishing protein binding sites.
To demonstrate SILIRID's utility in visualizing chemogenomic space.

Main Methods:

SILIRID descriptor generation from binary interaction fingerprints (IFPs).
Calculation of a 168-integer vector representing 8 interaction types across 20 amino acids and a cofactor.
Performance evaluation using similarity searches in the sc-PDB database.

Main Results:

SILIRID effectively characterizes protein-ligand interactions.
Similarity searches using SILIRID achieved performance comparable to state-of-the-art methods (ROC AUC ≈ 0.91).
SILIRID enabled visualization of the sc-PDB chemogenomic space, revealing clusters corresponding to protein types.

Conclusions:

SILIRID is an efficient and effective descriptor for protein-ligand interactions.
The descriptor facilitates the analysis and comparison of protein binding sites.
SILIRID aids in understanding the diversity of protein-ligand interactions within large databases.