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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

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:

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...

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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

Ligand B-Factor Index: A Metric for Prioritizing Protein-Ligand Complexes in Docking.

Liliana Halip¹, Cristian Neanu¹, Sorin Avram¹

¹Department of Computational Chemistry, "Coriolan Drăgulescu" Institute of Chemistry Timișoara, Romanian Academy, Timișoara, Romania.

Molecular Informatics

|September 11, 2025

Summary

A new metric, the ligand B-factor index (LBI), prioritizes protein-ligand complexes for docking by comparing atomic displacements. LBI shows moderate correlation with binding affinity and improves redocking success, aiding drug discovery.

Keywords:

B‐factor crystal‐structures docking scoring functions

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Last Updated: Jan 18, 2026

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Area of Science:

Computational chemistry
Cheminformatics
Drug discovery

Background:

Docking is a crucial structure-based cheminformatics tool in early drug discovery.
It predicts protein-ligand interactions, binding affinity, and identifies active compounds via virtual screening.
Existing metrics often overlook ligand flexibility, impacting docking accuracy.

Purpose of the Study:

Introduce the novel ligand B-factor index (LBI) for prioritizing protein-ligand complexes in docking.
Evaluate LBI's effectiveness in enhancing docking performance using the CASF-2016 dataset.
Assess LBI's correlation with experimental binding affinities and redocking success.

Main Methods:

Defined LBI as the ratio of median atomic B-factors between the binding site and the ligand.
Utilized the Comparative Assessment of Scoring Functions (CASF-2016) dataset for evaluation.
Compared LBI's performance against other metrics and docking scoring functions.

Main Results:

LBI demonstrated a moderate correlation (Spearman ρ ~ 0.48) with experimental binding affinities.
LBI outperformed several standard docking scoring functions in predicting binding.
The metric correlated with improved redocking success (RMSD < 2 Å), highlighting its ligand-centric value.

Conclusions:

LBI is a novel, interpretable, and easily computable metric for prioritizing protein-ligand complexes in docking.
It offers advantages over protein B-factor and resolution metrics, though its virtual screening utility requires further study.
LBI is freely available, facilitating its application in structure-based cheminformatics.