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Related Concept Videos

Conformations of Butane02:20

Conformations of Butane

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 degenerate and have...
Conformations of Ethane and Propane02:18

Conformations of Ethane and Propane

In an organic molecule, free rotation about the carbon-carbon single bond results in energetically different conformers of the molecule. Due to this rotation, called the internal rotation, ethane has two major conformations — staggered and eclipsed.
Staggered conformation is a low energy and more stable conformation with the C-H bonds on the front carbon placed at 60°dihedral angles relative to the C-H bonds on the back carbon, leading to a reduced torsional strain. In staggered ethane, 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.
Chair Conformation of Cyclohexane02:02

Chair Conformation of Cyclohexane

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 staggered...
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,...
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.

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Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches
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Published on: October 13, 2022

All-atom chain-building by optimizing MODELLER energy function using conformational space annealing.

Keehyoung Joo1, Jinwoo Lee, Joo-Hyun Seo

  • 1School of Computational Sciences, Korea Institute for Advanced Study, Seoul 130-722, Korea.

Proteins
|December 18, 2008
PubMed
Summary

Rigorous optimization of the MODELLER energy function using conformational space annealing (CSA) significantly improves protein side-chain modeling accuracy. This MODELLERCSA method outperforms standard MODELLER and other strategies for accurate all-atom model generation.

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Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Modeling

Background:

  • Accurate protein modeling is crucial for understanding biological function.
  • Standard protein modeling software like MODELLER has limitations in energy optimization.
  • Improving side-chain accuracy is a key challenge in all-atom protein modeling.

Purpose of the Study:

  • To investigate the effect of rigorous energy function optimization on protein all-atom chain-building.
  • To enhance the standard MODELLER procedure using global optimization methods.
  • To assess the performance of the novel MODELLERCSA method for protein modeling.

Main Methods:

  • Applied conformational space annealing (CSA), a global optimization method, to the MODELLER energy function.
  • Developed and tested the MODELLERCSA method on benchmark datasets (HOMSTRAD and CASP7).
  • Evaluated side-chain and backbone accuracy improvements compared to standard MODELLER and other methods.

Main Results:

  • MODGELLERCSA achieved significant improvements in side-chain modeling accuracy: 10.7% for chi(1) and 14.5% for chi(1) + chi(2).
  • Backbone accuracy improvements were less prominent and achievable with standard MODELLER strategies.
  • MODGELLERCSA's side-chain accuracy surpassed extensive MODELLER strategies, SCWRL3, and rotamer copying.

Conclusions:

  • Thorough optimization of the MODELLER energy function, as implemented in MODELLERCSA, leads to accurate all-atom protein models.
  • A strong correlation exists between MODELLER energy and side-chain accuracy.
  • MODGELLERCSA provides a superior approach for side-chain modeling when template alignments are reliable.