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Related Concept Videos

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.

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Related Experiment Video

Updated: May 8, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

SIMS: a hybrid method for rapid conformational analysis.

Bryant Gipson1, Mark Moll, Lydia E Kavraki

  • 1Department of Computer Science, Rice University, Houston, Texas, United States of America.

Plos One
|August 13, 2013
PubMed
Summary
This summary is machine-generated.

A new hybrid modeling tool, the Structured Intuitive Move Selector (sims), rapidly analyzes large-scale protein conformational changes by combining precise energy calculations with approximate sampling methods. This computational biology advance offers fast and accurate insights into protein flexibility.

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Related Experiment Videos

Last Updated: May 8, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

Area of Science:

  • Computational Biology
  • Biophysics
  • Structural Biology

Background:

  • Proteins perform complex biological functions through structural changes.
  • Accurately modeling these conformational changes is computationally intensive.
  • Existing methods are either physically accurate but slow, or fast but approximate.

Purpose of the Study:

  • Introduce a novel hybrid modeling tool, the Structured Intuitive Move Selector (sims).
  • Bridge the gap between computationally demanding and approximate protein modeling methods.
  • Enable rapid and accurate analysis of large-scale protein conformational variability.

Main Methods:

  • Developed a hybrid modeling tool integrating a robotics motion planning algorithm with a protein modeling library.
  • Employed generically defined moves for conformational sampling.
  • Utilized expansive probabilistic conformational exploration.
  • Combined precise energy calculations with approximate or specialized sampling routines.

Main Results:

  • Demonstrated rapid and accurate analysis of protein conformational variability.
  • Successfully applied sims to three distinct biological problems.
  • Identified active residues in Cyanovirin-N.
  • Explored long-range coordinated motions in Ribose-Binding Protein.
  • Discovered a transient conformational state of Maltose-Binding Protein.

Conclusions:

  • Sims provides a fast and accurate framework for analyzing protein flexibility.
  • The tool effectively integrates precise energy calculations with efficient conformational sampling.
  • Offers a valuable advancement for computational biology research.