Related Experiment Video
Updated: Jan 22, 2026
09:49
Routine Collection of High-Resolution cryo-EM Datasets Using 200 KV Transmission Electron Microscope
Published on: March 16, 2022
5.9K
Namdinator - automatic molecular dynamics flexible fitting of structural models into cryo-EM and crystallography
Rune Thomas Kidmose1, Jonathan Juhl1, Poul Nissen1
1Centre for Structural Biology, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, Aarhus, DK-8000, Denmark.
Iucrj
|July 19, 2019
Summary
Namdinator automates molecular dynamics flexible fitting and real-space refinement for atomic models in low-resolution cryo-electron microscopy (cryo-EM) and crystallography maps. This tool significantly improves model accuracy and geometry for structural biology.
Area of Science:
- Structural Biology
- Computational Biology
- Biophysics
Background:
- Atomic model building into experimental maps is crucial but challenging for low-resolution data.
- Existing methods can be time-consuming and prone to errors.
Purpose of the Study:
- To present Namdinator, an automated pipeline for molecular dynamics flexible fitting and real-space refinement.
- To provide an easy-to-use tool for improving atomic models in cryo-electron microscopy (cryo-EM) and crystallography density maps.
Main Methods:
- Developed an automated pipeline integrating molecular dynamics flexible fitting and real-space refinement.
- Benchmarked Namdinator against 39 deposited cryo-EM models and maps.
Main Results:
- Namdinator improved models in 87% of tested cases (34 out of 39).
- Observed significant reductions in atomic clashes and improvements in model-to-map fit and geometry.
- Demonstrated ability to model large-scale conformational changes.
Conclusions:
- Namdinator is a fast, easy-to-use tool for structural model building and refinement.
- The software benefits structural biologists of all skill levels and is available as a web service or local tool.
Related Concept Videos
01:13Induced-fit Model
88.9K
Most chemical reactions in cells require enzymes—biological catalysts that speed up the reaction without being consumed or permanently changed. They reduce the activation energy needed to convert the reactants into products. Enzymes are proteins, that usually work by binding to a substrate—a reactant molecule that they act upon.
Enzymes exhibit substrate specificity, meaning that they can only bind to certain substrates. This is mainly determined by the shape and chemical...
Enzymes exhibit substrate specificity, meaning that they can only bind to certain substrates. This is mainly determined by the shape and chemical...
88.9K
02:18X-ray Crystallography
25.8K
The size of the unit cell and the arrangement of atoms in a crystal may be determined from measurements of the diffraction of X-rays by the crystal, termed X-ray crystallography.
Diffraction
Diffraction is the change in the direction of travel experienced by an electromagnetic wave when it encounters a physical barrier whose dimensions are comparable to those of the wavelength of the light. X-rays are electromagnetic radiation with wavelengths about as long as the distance between neighboring...
Diffraction
Diffraction is the change in the direction of travel experienced by an electromagnetic wave when it encounters a physical barrier whose dimensions are comparable to those of the wavelength of the light. X-rays are electromagnetic radiation with wavelengths about as long as the distance between neighboring...
25.8K
01:18Structure of Benzene: Molecular Orbital Model
12.2K
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).
12.2K
02:00Molecular Models
43.6K
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.
43.6K
02:34Molecular Structure and Acidity
20.4K
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...
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...
20.4K
03:05Acid Strength and Molecular Structure
32.9K
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...
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...
32.9K