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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...
Metal-Ligand Bonds02:51

Metal-Ligand Bonds

The hemoglobin in the blood, the chlorophyll in green plants, vitamin B-12, and the catalyst used in the manufacture of polyethylene all contain coordination compounds. Ions of the metals, especially the transition metals, are likely to form complexes.
In these complexes, transition metals form coordinate covalent bonds, a kind of Lewis acid-base interaction in which both of the electrons in the bond are contributed by a donor (Lewis base) to an electron acceptor (Lewis acid). The Lewis acid in...
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...
Complexometric Titration: Ligands00:43

Complexometric Titration: Ligands

Different monodentate and polydentate ligands are used as complexing agents in complexometric titration reactions. The formation of complexes by mono- and bidentate ligands involves two or more intermediate steps, limiting their use as complexing agents. In comparison, polydentate ligands can form complexes with metal ions in a single-step process, facilitating sharper end points. This means polydentate ligands, such as amino carboxylic acid derivatives, are most commonly employed in...

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Updated: May 23, 2026

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
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Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Handling ligands with Coot.

Judit É Debreczeni1, Paul Emsley

  • 1Structure and Biophysics, DS, AstraZeneca, Alderley Park SK10 4TG, England. judit.debreczeni@astrazeneca.com

Acta Crystallographica. Section D, Biological Crystallography
|April 17, 2012
PubMed
Summary
This summary is machine-generated.

Coot now includes new tools for small molecule ligands, aiding in their manipulation and validation. These features enhance the analysis of ligand chemistry and fitting within biological macromolecules.

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Area of Science:

  • Structural Biology
  • Computational Chemistry
  • Biochemistry

Background:

  • Coot is a widely used molecular graphics application for macromolecular model building and validation.
  • Existing Coot functionalities primarily focus on proteins and nucleic acids.

Purpose of the Study:

  • To introduce and describe new tools integrated into Coot for handling small molecules (ligands).
  • To enhance the capabilities of Coot for ligand manipulation and validation in structural biology workflows.

Main Methods:

  • Integration of PRODRG for ligand processing.
  • Implementation of subgraph isomorphism algorithms for chemical structure comparison.
  • Development of tools for ligand chemistry representation, fitting, and analysis.

Main Results:

  • Coot now supports comprehensive manipulation and validation of small molecule ligands.
  • New functionalities facilitate detailed analysis of ligand interactions and conformations.
  • The enhanced Coot application streamlines the process of incorporating and refining ligand models.

Conclusions:

  • The expanded toolkit in Coot significantly improves its utility for researchers working with ligands.
  • These advancements facilitate more accurate and efficient structural analysis involving both macromolecules and small molecules.