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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...

The Equilibrium Binding Constant and Binding Strength

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:

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Related Experiment Video

Updated: May 11, 2026

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Published on: December 1, 2020

Open-source platform to benchmark fingerprints for ligand-based virtual screening.

Sereina Riniker¹, Gregory A Landrum

¹Novartis Institutes for BioMedical Research, Basel, Switzerland. gregory.landrum@novartis.com.

Journal of Cheminformatics

|June 1, 2013

Summary

This summary is machine-generated.

A new platform standardizes the benchmarking of 2D molecular fingerprints for virtual screening. Most fingerprints performed similarly, with only baseline methods showing statistically significant differences.

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Last Updated: May 11, 2026

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

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Published on: December 1, 2020

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Area of Science:

Computational chemistry
Cheminformatics
Drug discovery

Background:

Ligand-based virtual screening relies on molecular similarity searches.
Numerous 2D fingerprints exist, but performance varies with datasets and similarity measures.
Lack of standardized benchmarking hinders comparison of new and existing methods.

Purpose of the Study:

To introduce a standardized, open-source platform for benchmarking 2D molecular fingerprints.
To enable reproducible and statistically valid comparisons of similarity-search methods.
To facilitate the evaluation of different fingerprints and similarity measures in virtual screening.

Main Methods:

Developed an open-source platform with source code and structural data.
Utilized publicly available datasets comprising actives and inactives.
Employed randomly selected query molecules for statistically valid comparisons.
Assessed 12 standard fingerprints and 2 baseline fingerprints using 7 evaluation methods.

Main Results:

High correlations observed among the 12 standard 2D fingerprints.
Statistical analysis revealed only baseline fingerprints differed significantly from others.
Six out of seven evaluation methods showed high correlations, indicating methodological similarities.

Conclusions:

The developed platform provides a robust standard for 2D fingerprint benchmarking.
Most commonly used 2D fingerprints exhibit similar performance in virtual screening.
Evaluation methods for similarity searching are largely interchangeable, despite apparent differences.