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Related Concept Videos

Conformations of Cycloalkanes02:29

Conformations of Cycloalkanes

12.2K
Adolf von Baeyer attempted to explain the instabilities of small and large cycloalkane rings using the concept of angle strain — the strain caused by the deviation of bond angles from the ideal 109.5° tetrahedral value for sp3  hybridized carbons. However, while cyclopropane and cyclobutane are strained, as expected from their highly compressed bond angles, cyclopentane is more strained than predicted, and cyclohexane is virtually strain-free. Hence, Baeyer’s theory that...
12.2K
Conformations of Cyclohexane02:11

Conformations of Cyclohexane

12.2K
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...
12.2K
Conformations of Butane02:20

Conformations of Butane

14.3K
Unlike ethane and propane that have only two major conformations, butane has more than two conformers. The staggered form of butane in which the bulky methyl groups on the two carbons are placed on opposite sides, that is, at a dihedral angle of 180°, is the lowest energy, most stable form — called the anti conformer. This conformation is stabilized due to the absence of steric repulsion between the largely spaced out methyl groups. The other two staggered conformations are...
14.3K
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

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

1.4K
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.
1.4K
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

992
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...
992
Chair Conformation of Cyclohexane02:02

Chair Conformation of Cyclohexane

16.2K
The chair conformation is the most stable form of cyclohexane due to the absence of angle and torsional strain. The absence of angle strain is a result of cyclohexane’s bond angle being very close to the ideal tetrahedral bond angle of 109.5° in its chair conformer. Similarly, the torsional strain is also absent owing to the perfectly staggered arrangement of bonds.
The hydrogen atoms linked to carbons are arranged in two different axial and equatorial orientations to achieve this...
16.2K

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ConforNets: Latents-Based Conformational Control in OpenFold3.

Minji Lee1, Colin Kalicki2, Minkyu Jeon3

  • 1Department of Computer Science, Columbia University, NY, USA.

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|May 4, 2026
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Summary
This summary is machine-generated.

ConforNets enhance AlphaFold3 (AF3) models to predict multiple protein structures by perturbing latent representations. This method efficiently generates alternate protein states and enables conformational transfer across protein families.

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Area of Science:

  • Computational Biology
  • Structural Biology
  • Protein Bioinformatics

Background:

  • AlphaFold (AF) models excel at predicting single protein conformations.
  • Existing methods struggle to capture diverse, biologically relevant alternate protein states.
  • Current approaches for eliciting conformational variability are inefficient and inconsistent.

Purpose of the Study:

  • To identify optimal methods for perturbing latent representations in AlphaFold3 (AF3) architecture.
  • To develop a novel mechanism for controlling protein conformational dynamics in AF3 models.
  • To improve the prediction of alternate protein conformations and enable conformational transfer.

Main Methods:

  • Investigated optimal perturbation strategies within the AF3 latent space.
  • Developed ConforNets: channel-wise affine transforms of pre-Pairformer pair latents.
  • Applied ConforNets for unsupervised generation of alternate states and supervised conformational transfer.

Main Results:

  • ConforNets achieve state-of-the-art success rates on multi-state protein structure benchmarks.
  • ConforNets globally modulate AF3 representations, enabling reusability across different proteins.
  • Successfully demonstrated conformational transfer, inducing conserved changes across protein families.

Conclusions:

  • ConforNets provide an efficient and effective mechanism for controlling protein conformational diversity in AF3.
  • This approach significantly advances the prediction of multiple protein structures and functional states.
  • ConforNets pave the way for novel applications in protein design and engineering.