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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...

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Related Experiment Video

Updated: May 25, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

AsteriX: a Web server to automatically extract ligand coordinates from figures in PDF articles.

V Lounnas1, G Vriend

  • 1CMBI NCMLS Radboud University, Nijmegen Medical Centre, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands. v-lounnas@unicancer.fr

Journal of Chemical Information and Modeling
|February 4, 2012
PubMed
Summary

This study introduces AsteriX, a web server that automatically reconstructs 3D ligand coordinates from 2D chemical diagrams in PDF files, aiding drug design. It successfully identifies and reconstructs many ligand structures, with user correction options available.

Related Experiment Videos

Last Updated: May 25, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Area of Science:

  • Computational chemistry
  • Cheminformatics
  • Drug discovery

Background:

  • Chemical structure coordinates are vital for drug design.
  • Ligand coordinates are often found in scientific literature, requiring manual reconstruction.
  • Manual reconstruction is a time-consuming process.

Purpose of the Study:

  • To develop a web server, AsteriX, for reconstructing 3D ligand coordinates from 2D images in PDF files.
  • To automate the extraction of ligand information from scientific literature.

Main Methods:

  • AsteriX analyzes PDF images to identify potential ligand structures.
  • It extracts connectivity and atom type information to reconstruct 3D coordinates.
  • The server allows user augmentation and correction of partially reconstructed 3D structures.

Main Results:

  • AsteriX identified 88% of 3249 ligand structures as chemical diagrams in test articles.
  • Approximately 50% of identified diagrams were correctly interpreted as 3D structures.
  • An additional third of structures required only minor manual corrections.

Conclusions:

  • AsteriX automates the reconstruction of 3D ligand coordinates from 2D images, significantly reducing manual effort.
  • The web server provides a valuable tool for drug design by facilitating access to ligand coordinates from literature.
  • User-corrected and validated 3D reconstructions are made freely available in common drug design formats.