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Related Concept Videos

Crystal Field Theory - Octahedral Complexes02:58

Crystal Field Theory - Octahedral Complexes

Crystal Field Theory
To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
CFT focuses on...
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...
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...
Molecular Models02:00

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.

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Related Experiment Video

Updated: May 14, 2026

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Visualizing ligand molecules in Twilight electron density.

Christian X Weichenberger1, Edwin Pozharski, Bernhard Rupp

  • 1Center for Biomedicine, European Academy of Bozen/Bolzano, Viale Druso 1, I-39100 Bozen/Bolzano, Italy. christian.weichenberger@eurac.edu

Acta Crystallographica. Section F, Structural Biology and Crystallization Communications
|February 7, 2013
PubMed
Summary
This summary is machine-generated.

Twilight is a new script that helps analyze protein-ligand complexes. It assesses the fit of atomic models to electron density maps, aiding drug design and biological activity studies.

Keywords:
electron densityprotein–ligand structuresreal-space correlationvalidation

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Area of Science:

  • Structural Biology
  • Computational Biology
  • Drug Design

Background:

  • X-ray crystallography generates 3D protein models from electron-density maps.
  • Real-space correlation coefficient (RSCC) objectively measures atom coordinate fit to electron density.
  • Protein-ligand complexes are crucial for understanding biological activity and drug development.

Purpose of the Study:

  • To develop a tool for analyzing and visualizing protein-ligand complexes.
  • To assess the reliability of ligand-structure modeling by evaluating electron-density fit.
  • To provide objective measures for the quality of protein-ligand models in the Protein Data Bank (PDB).

Main Methods:

  • A standalone script named Twilight was developed.
  • Twilight analyzes 2815 protein-ligand complexes with ligand RSCC below 0.6.
  • It visualizes and annotates these complexes and any other PDB protein-ligand complex via the Uppsala Electron Density Server.

Main Results:

  • Twilight facilitates the objective assessment of ligand-structure model quality.
  • The script enables visualization and annotation of protein-ligand complexes.
  • It provides a standardized method for evaluating electron-density fit in structural models.

Conclusions:

  • Twilight offers a valuable resource for researchers studying protein-ligand interactions.
  • The tool helps mitigate subjective interpretation in electron-density fitting.
  • It supports more reliable drug design and biological activity investigations.