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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

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...

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Nano-Differential Scanning Fluorimetry for Screening in Fragment-based Lead Discovery

Nano-Differential Scanning Fluorimetry for Screening in Fragment-based Lead Discovery

Published on: May 16, 2021

Novel 2D fingerprints for ligand-based virtual screening.

Todd Ewing¹, J Christian Baber, Miklos Feher

¹Neurocrine Biosciences, 12790 El Camino Real, San Diego, California 92130, USA. tewing@neurocrine.com

Journal of Chemical Information and Modeling

|November 28, 2006

Summary

New 2D fingerprints enhance virtual screening for drug discovery. Modifications to feature types, counts, and property resolution improve performance in pharmaceutical research.

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Area of Science:

Medicinal Chemistry
Computational Chemistry
Drug Discovery

Background:

Virtual screening is crucial for identifying drug candidates.
Existing 2D fingerprints have limitations in accuracy and efficiency.
Optimizing molecular representation is key to improving screening outcomes.

Purpose of the Study:

To develop novel 2D molecular fingerprints for enhanced virtual screening.
To investigate the impact of specific design modifications on fingerprint performance.
To assess the utility of these fingerprints across different stages of drug discovery.

Main Methods:

Development of new 2D fingerprints incorporating overlapping pharmacophore features.
Inclusion of feature counts for both pharmacophore and structural fingerprints.
Adjustment of property description resolution within the fingerprints.
Evaluation using two distinct training sets representing different drug discovery phases.

Main Results:

All introduced design changes led to improved virtual screening performance.
Overlapping pharmacophore features enhanced the discriminatory power of the fingerprints.
Feature counts and adjusted property resolution contributed to better screening accuracy.
The new fingerprints demonstrated effectiveness across various drug discovery contexts.

Conclusions:

The developed 2D fingerprints represent a significant advancement for virtual screening.
These improved fingerprints can accelerate the identification of promising drug candidates.
The design principles can be applied to further refine molecular representation techniques in cheminformatics.