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Ligand Binding Sites

Ligand Binding Sites

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 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

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

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A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

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LIGSIFT: an open-source tool for ligand structural alignment and virtual screening.

Ambrish Roy¹, Jeffrey Skolnick¹

¹Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, GA 30076, USA.

Bioinformatics (Oxford, England)

|October 23, 2014

Summary

This summary is machine-generated.

A new algorithm, LIGSIFT, offers improved small molecule alignment and virtual screening by using statistical significance for scoring, overcoming limitations of traditional size-dependent methods.

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Area of Science:

Computational chemistry
Drug discovery
Bioinformatics

Background:

Shape-based alignment is crucial in computer-aided drug discovery.
Existing methods often use size-dependent similarity scores like Tanimoto coefficient.
These traditional metrics lack reporting on statistical significance and are affected by molecular size.

Purpose of the Study:

Introduce LIGSIFT, a novel open-source algorithm for ligand structure alignment and virtual screening.
Develop a size-independent scoring function based on statistical significance for enhanced virtual screening.
Address the limitations of existing shape-based alignment tools.

Main Methods:

Implemented LIGSIFT using Gaussian molecular shape overlay for rapid small molecule alignment.
Developed a novel scoring function that is independent of molecular size and relies on statistical significance.
Validated LIGSIFT performance against 40 protein targets using the Directory of Useful Decoys dataset.

Main Results:

LIGSIFT demonstrated strong performance in virtual screening tasks.
Achieved an average Area Under the ROC Curve (AUC) of 0.79.
Reported average Enrichment Factor (EF) of 20.8 and a Hit Rate (HR) of 59% in the top 1% of screened libraries.

Conclusions:

LIGSIFT provides an efficient and statistically robust approach for small molecule alignment and virtual screening.
The algorithm overcomes the drawbacks of size-dependent scoring functions.
LIGSIFT is freely available for academic use, promoting further research in drug discovery.