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Related Concept Videos

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.
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.
Conformations of Cyclohexane02:11

Conformations of Cyclohexane

Cyclohexane does not exist in a planar form due to the high angle and torsional strain it would experience in the planar structure. Instead, it adopts non-planar chair and boat conformations.
The chair form is the most stable and derives its name from its resemblance to the “easy chair.” In the chair conformation, two carbon atoms are arranged out-of-plane — one above and one below, minimizing the torsional strain. In the chair form, the bond angle is very close to the ideal tetrahedral value,...
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...
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...

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Related Experiment Video

Updated: Jun 28, 2026

Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

tCONCOORD-GUI: visually supported conformational sampling of bioactive molecules.

Daniel Seeliger1, Bert L De Groot

  • 1Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.

Journal of Computational Chemistry
|October 24, 2008
PubMed
Summary

A new graphical user interface (GUI) simplifies tCONCOORD simulations for analyzing bioactive molecule flexibility. This tool aids in setting up simulations and understanding conformational changes in computational biology.

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Area of Science:

  • Computational Biology
  • Molecular Modeling
  • Structural Bioinformatics

Background:

  • Conformational flexibility in bioactive molecules presents a significant challenge for computational biology.
  • tCONCOORD is a method that generates structural ensembles using geometrical principles to predict protein flexibility and essential degrees of freedom.

Purpose of the Study:

  • To develop a graphical user interface (GUI) for tCONCOORD to simplify simulation setup and enhance structural analysis.
  • To provide users with interactive control over constraint definition for biased conformational sampling.

Main Methods:

  • Development of a user-friendly GUI for the tCONCOORD software.
  • Implementation of interactive features for defining rigid/flexible regions and applying artificial constraints.
  • Utilizing geometrical considerations for generating molecular structure ensembles.

Main Results:

  • The tCONCOORD-GUI substantially facilitates the setup of tCONCOORD simulations.
  • The interface provides valuable insights into structure analysis and constraint definition.
  • Users can interactively control simulation parameters for biased sampling of conformational space.

Conclusions:

  • The tCONCOORD-GUI offers a versatile environment for tCONCOORD simulations, molecular modeling, and structure analysis.
  • The software is freely distributed, promoting accessibility in computational biology research.