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Related Concept Videos

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...
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,...
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...
Fischer Projections02:18

Fischer Projections

Learning to draw Fischer projections of molecules and understanding their relevance plays a crucial role in the visual depiction of organic molecules. A Fischer projection is a two-dimensional projection on a planar surface to simplify the three-dimensional wedge–dash representation of molecules. This is especially helpful in the case of molecules with multiple chiral centers that can be difficult to draw. Here, all the bonds of interest are represented as horizontal or vertical lines. While...
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...
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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A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Subdivision approach to target-constrained conformational searching.

Ming Zhang1, Liqun Wang, David Maxwell

  • 1Departments of Biostatistics and Applied Mathematics, The University of Texas M.D. Anderson Cancer Center Houston TX 77030 USA. (mzhang@mdanderson.org).

Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference
|February 7, 2007
PubMed
Summary

This study introduces two novel subdivision methods for target-constrained conformational searching. These algorithms approximate solutions, offering potential speed and quality improvements for molecular modeling applications.

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Area of Science:

  • Computational chemistry
  • Molecular modeling
  • Algorithm development

Background:

  • Conformational searching is crucial for understanding molecular behavior.
  • Existing methods for conformational searching can be computationally intensive.
  • Improvements in speed and accuracy are highly desirable.

Purpose of the Study:

  • To develop and evaluate new algorithms for target-constrained conformational searching.
  • To address limitations in current conformational searching techniques.
  • To present the performance of novel approximation methods.

Main Methods:

  • Developed two subdivision-based methods for conformational searching.
  • Focused on approximating solutions rather than finding exact solutions.
  • Implemented and tested algorithms for target-constrained problems.

Main Results:

  • Demonstrated the performance of the two proposed subdivision methods.
  • Showcased the effectiveness of approximation strategies in conformational searching.
  • Provided quantitative data on the methods' performance.

Conclusions:

  • The developed subdivision methods offer a viable approach to target-constrained conformational searching.
  • Approximation strategies can significantly impact the efficiency of conformational searches.
  • Further research can build upon these methods for enhanced molecular modeling tools.