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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...

Ligand Binding and Linkage

Ligand Binding and Linkage

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...

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...

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Related Experiment Video

Updated: Dec 28, 2025

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source

Published on: May 29, 2021

InterLig: improved ligand-based virtual screening using topologically independent structural alignments.

Claudio Mirabello¹, Björn Wallner¹

¹Division of Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, Linköping 581 83, Sweden.

Bioinformatics (Oxford, England)

|February 13, 2020

Summary

This summary is machine-generated.

Computational drug discovery uses virtual screening to identify promising molecules. A new method, InterLig, offers accurate 3D molecule comparison and superposition for improved ligand-based virtual screening.

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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:

Computational chemistry
Drug discovery
Cheminformatics

Background:

Drug discovery increasingly relies on computational methods for efficiency.
Ligand-based virtual screening is crucial when protein targets are unknown.
3D similarity methods enable scaffold hopping and molecular superposition.

Purpose of the Study:

Introduce InterLig, a novel method for small molecule comparison and superposition.
Evaluate InterLig's performance against existing 3D similarity methods.

Main Methods:

Utilizes topologically independent alignments of atoms for molecule comparison.
Employs a standard benchmark dataset for performance testing.

Main Results:

InterLig demonstrates favorable comparison to state-of-the-art 3D methods.
The method accurately compares and superimposes small molecules.

Conclusions:

InterLig provides an accurate and effective approach for ligand-based virtual screening.
The developed method advances computational drug discovery capabilities.