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Related Concept Videos

Ligand Binding Sites02:40

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 Sites02:40

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 Linkage00:49

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 the...
Conserved Binding Sites01:49

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 analyses the...
The Equilibrium Binding Constant and Binding Strength02:18

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: Jun 2, 2026

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
10:29

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Published on: May 9, 2025

LiraSearch-ultrafast ligand shape and electrostatic matching server.

Rinaldo W Montalvão1, Simon Bray2, Marcos Veríssimo-Alves3

  • 1Gain Therapeutics Sucursal España, Gain Therapeutics, Barcelona Science Park, Barcelona, 08028, Spain.

Bioinformatics Advances
|June 1, 2026
PubMed
Summary
This summary is machine-generated.

LiraSearch utilizes spherical harmonics to rapidly compare 3D molecular shapes and electrostatics for drug discovery. This method enables efficient virtual screening of large compound libraries, identifying diverse active molecules without explicit alignment.

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

Published on: December 1, 2020

Related Experiment Videos

Last Updated: Jun 2, 2026

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
10:29

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Published on: May 9, 2025

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
08:31

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

Published on: December 1, 2020

Area of Science:

  • Computational chemistry
  • Cheminformatics
  • Drug discovery

Background:

  • Spherical harmonics are effective for molecular shape and electrostatic comparison in virtual screening.
  • Efficient methods are needed for comparing large compound libraries.

Purpose of the Study:

  • To present LiraSearch, a high-performance implementation and web server for molecular similarity searching.
  • To encode and compare 3D molecular shapes and electrostatic potential (ESP) surfaces using spherical harmonics expansions.

Main Methods:

  • Transforming molecular surfaces into compact, low-dimensional spherical harmonics descriptors.
  • Utilizing rotational invariance of spherical harmonics for alignment-free similarity calculations.
  • Developing an efficient screening pipeline for rapid similarity searches.

Main Results:

  • LiraSearch enables rapid similarity calculations between query molecules and large compound libraries.
  • The representation is robust to conformational variation and identifies diverse active compounds.
  • High retrieval performance is achieved with compact descriptors and low expansion orders.

Conclusions:

  • LiraSearch provides a scalable, mathematically rigorous approach to ligand similarity searching.
  • The framework supports early-stage hit discovery and downstream applications like docking.
  • It facilitates scaffold hopping by identifying structurally diverse compounds with similar pharmacophores.