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Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
One-Compartment Open Model: Wagner-Nelson and Loo Riegelman Method for ka Estimation01:24

One-Compartment Open Model: Wagner-Nelson and Loo Riegelman Method for ka Estimation

This lesson introduces two critical methods in pharmacokinetics, the Wagner-Nelson and Loo-Riegelman methods, used for estimating the absorption rate constant (ka) for drugs administered via non-intravenous routes. The Wagner-Nelson method relates ka to the plasma concentration derived from the slope of a semilog percent unabsorbed time plot. However, it is limited to drugs with one-compartment kinetics and can be impacted by factors like gastrointestinal motility or enzymatic degradation.
On...
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 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.
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Molecular Comparison of Gases, Liquids, and Solids02:26

Molecular Comparison of Gases, Liquids, and Solids

Particles in a solid are tightly packed together (fixed shape) and often arranged in a regular pattern; in a liquid, they are close together with no regular arrangement (no fixed shape); in a gas, they are far apart with no regular arrangement (no fixed shape). Particles in a solid vibrate about fixed positions (cannot flow) and do not generally move in relation to one another; in a liquid, they move past each other (can flow) but remain in essentially constant contact; in a gas, they move...
Kendall's Coefficient of Concordance01:20

Kendall's Coefficient of Concordance

Kendall's Coefficient of Concordance (W), also known as Kendall's W, is a non-parametric statistical measure used to assess the agreement or concordance between multiple raters or judges when they rank a set of items. It is often used when you have ordinal data (ranks) and you want to see if there is consistency or consensus among the raters. It is widely applied in research areas such as psychology, medicine, and social sciences, where multiple judges are asked to rank or rate subjects or...

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Related Experiment Video

Updated: May 15, 2026

VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma
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Comparing Conformational Ensembles Using the Kullback-Leibler Divergence Expansion.

Christopher L McClendon1, Lan Hua, Abriela Barreiro

  • 1Graduate Group in Biophysics, University of California San Francisco.

Journal of Chemical Theory and Computation
|January 15, 2013
PubMed
Summary

This study introduces a novel thermodynamical method using Kullback-Leibler Divergence to analyze protein structure and dynamics changes. The approach accurately predicts effects of mutations or ligand binding, aiding in understanding protein behavior.

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Published on: July 16, 2017

Area of Science:

  • Computational Biology
  • Biophysics
  • Structural Biology

Background:

  • Understanding protein structure-dynamics relationships is crucial for drug discovery and protein engineering.
  • Existing methods may not fully capture subtle macromolecular changes induced by perturbations.
  • Molecular dynamics (MD) simulations offer insights but require robust analytical tools.

Purpose of the Study:

  • To develop a thermodynamical approach for identifying macromolecular structural and dynamic changes.
  • To connect local population shifts in protein torsion angles to free energy landscape alterations.
  • To provide a novel computational tool for analyzing MD simulations under different conditions.

Main Methods:

  • Utilized an expansion of the Kullback-Leibler Divergence, linking torsion angle population shifts to free energy changes.
  • Applied a first-order approximation of the Kullback-Leibler Divergence expansion to MD simulations.
  • Analyzed four protein systems undergoing ligand binding or pH titration.

Main Results:

  • The method successfully identified local structural and dynamic changes in proteins.
  • Results showed qualitative agreement with experimental data, including NMR chemical shift perturbations.
  • The approach yielded clear, low-background results, facilitating analysis.

Conclusions:

  • The developed thermodynamical approach offers a powerful and extendable method for analyzing protein dynamics.
  • It has the potential to become a standard tool for comparative MD simulation studies.
  • The MutInf package implements this method, enhancing its accessibility for researchers.