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Related Concept Videos

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...
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...
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...

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Related Experiment Video

Updated: May 30, 2026

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Open3DALIGN: an open-source software aimed at unsupervised ligand alignment.

Paolo Tosco1, Thomas Balle, Fereshteh Shiri

  • 1Department of Drug Science and Technology, University of Turin, Italy. paolo.tosco@unito.it

Journal of Computer-Aided Molecular Design
|July 28, 2011
PubMed
Summary
This summary is machine-generated.

Open3DALIGN is a new open-source software for molecular alignment and conformer generation. Its unsupervised methods and parallelization enable efficient, automated drug discovery workflows.

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

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Related Experiment Videos

Last Updated: May 30, 2026

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

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

Published on: June 20, 2025

Area of Science:

  • Computational chemistry
  • Cheminformatics
  • Structural bioinformatics

Background:

  • Molecular alignment is crucial for drug discovery and understanding structure-activity relationships.
  • Existing methods may lack efficiency or flexibility for high-throughput screening.

Purpose of the Study:

  • To present Open3DALIGN, an open-source software for conformer generation and unsupervised molecular alignment.
  • To provide a versatile tool for automated cheminformatics workflows.

Main Methods:

  • Implementation of various algorithms for single and multi-conformation superimpositions.
  • Alignment based on pharmacophores, heavy atoms, or combined approaches.
  • Validation using eight established datasets.

Main Results:

  • Successful validation of implemented alignment methods on comprehensive datasets.
  • High computational performance achieved through efficient parallelization.
  • Demonstration of unsupervised alignment capabilities.

Conclusions:

  • Open3DALIGN is a validated, high-performance software for molecular alignment.
  • Its unsupervised nature and scriptable interface are ideal for automated, high-throughput cheminformatics.
  • The software facilitates efficient drug discovery and structural analysis.