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Related Concept Videos

Molecular Structure and Acidity02:34

Molecular Structure and Acidity

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An acid can be deprotonated to form a conjugate base or an anion. If the produced anion is more stable, then the acid is stronger. On the contrary, if the anion is unstable, then the acid is weaker. Hence, to determine the acidity of the compound, the stability of its conjugate base is studied using various factors.
The size effect explains the change in atomic size on acidity. When comparing the acids formed from elements that belong to the same column in the periodic table, their atomic sizes...
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Acid Strength and Molecular Structure03:05

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Binary Acids and Bases
In the absence of any leveling effect, the acid strength of binary compounds of hydrogen with nonmetals (A) increases as the H-A bond strength decreases down a group in the periodic table. For group 17, the order of increasing acidity is HF < HCl < HBr < HI. Likewise, for group 16, the order of increasing acid strength is H2O < H2S < H2Se < H2Te. Across a row in the periodic table, the acid strength of binary hydrogen compounds increases with increasing...
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Lewis Structures of Molecular Compounds and Polyatomic Ions02:54

Lewis Structures of Molecular Compounds and Polyatomic Ions

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To draw Lewis structures for complicated molecules and molecular ions, it is helpful to follow a step-by-step procedure as outlined:
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Correlations02:20

Correlations

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Correlation means that there is a relationship between two or more variables (such as ice cream consumption and crime), but this relationship does not necessarily imply cause and effect. When two variables are correlated, it simply means that as one variable changes, so does the other. We can measure correlation by calculating a statistic known as a correlation coefficient. A correlation coefficient is a number from -1 to +1 that indicates the strength and direction of the relationship between...
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Structure of Benzene: Molecular Orbital Model01:18

Structure of Benzene: Molecular Orbital Model

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According to the molecular orbital (MO) model, benzene has a planar structure with a regular hexagon of six sp2 hybridized carbons. As shown in Figure 1, each carbon is bonded to three other atoms with C–C–C and H–C–C bond angles of 120°. The C–H bond length is 109 pm, and the C–C bond length is 139 pm which is midway between the single bond length of sp3 hybridized carbons (154 pm) and sp2 hybridized carbons (133 pm).
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Correlation and Causation01:27

Correlation and Causation

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Statistical tests can calculate whether there is a relationship, or correlation, between independent and dependent variables. An indirect relationship of the variables signifies a correlation, while a direct relationship shows causation. If it is determined that no connection exists between the variables, then the correlation is a coincidence.
Correlation versus Causation
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Related Experiment Video

Updated: Jan 28, 2026

Correlative Microscopy for 3D Structural Analysis of Dynamic Interactions
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Correlative Microscopy for 3D Structural Analysis of Dynamic Interactions

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Automated cryo-EM structure refinement using correlation-driven molecular dynamics.

Maxim Igaev1, Carsten Kutzner1, Lars V Bock1

  • 1Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.

Elife
|March 5, 2019
PubMed
Summary
This summary is machine-generated.

We developed a new automated method, correlation-driven molecular dynamics (CDMD), to refine atomic models using cryo-electron microscopy (cryo-EM) maps. CDMD improves structural accuracy and outperforms existing methods for cryo-EM model refinement.

Keywords:
cryo-EMmolecular biophysicsmolecular dynamicsnonestructural biologystructure refinement

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Area of Science:

  • Structural biology
  • Computational biophysics

Background:

  • Cryo-electron microscopy (cryo-EM) enables high-resolution structural determination of biomolecules.
  • Accurate atomic model building into cryo-EM maps is crucial for interpreting structural data.

Purpose of the Study:

  • To develop an automated method for refining atomistic models into cryo-EM maps.
  • To assess the performance of the new method across diverse systems and resolutions.

Main Methods:

  • Correlation-driven molecular dynamics (CDMD) utilizing a chemically accurate force field and thermodynamic sampling.
  • Gradual increase in resolution and map-model agreement, coupled with simulated annealing.
  • Automated refinement without manual intervention or specialized restraints.

Main Results:

  • CDMD effectively refines atomistic models into cryo-EM maps from subnanometer to near-atomic resolution.
  • The method demonstrates high model accuracy and minimizes overfitting across various test cases.
  • CDMD outperforms several established refinement methods in objective comparisons.

Conclusions:

  • CDMD provides a robust and automated approach for high-quality cryo-EM model refinement.
  • The method enhances the interpretation of cryo-EM data by generating accurate atomic models.
  • CDMD represents a significant advancement in computational structural biology workflows.