Molecular Dynamics Analysis Service

Molecular dynamics simulation is the closest simulation method to experimental conditions in molecular simulation. It can give the microscopic evolution process of the system from the atomic level, intuitively show the mechanism and law of the occurrence of experimental phenomena, and promote our research to be more efficient and economical. The development is more predictable. Therefore, molecular dynamics simulation is playing an increasingly important role in the research of biology, pharmacy, chemistry, and materials science. Therefore, it is a research that is worth learning and adopting.

What problem can be solved by MD simulations?

• Compare the protein characteristics of wild-type and mutant proteins.
• The mechanism of ligand-receptor binding, we can put the ligand on the receptor to simulate the combination of the two in the natural state.
• With the development of lipid force field, we can also study the interaction between protein and membrane (lipid force field).
• The mechanism of protein folding, control the temperature, so that the protein folds and unfolds by itself.

Overall solutions

• Binding free energy calculations

After running MD, there is no doubt that it needs to be analyzed. The calculation of binding free energy is an indispensable part. There is an energy difference between the free state and the bound state of the ligand and the receptor. This energy difference can be used to measure the intimacy of the binding between them.

Figure 1. Binding free energy.

• Hydrogen bond analysis

Hydrogen bond analysis is an analysis we often do after running molecular dynamics simulations. The hydrogen bond is a weak force that forms a special type of dipole-dipole attraction. When a hydrogen atom and a lone pair of electrons existing in a strongly electronegative atom bond to another electronegative atom, a hydrogen atom will appears.

• Cluster analysis

Cluster analysis is the main task of exploratory data mining and a common technique for statistical data analysis. It has been used in many fields, including pattern recognition, image analysis, information retrieval, bioinformatics, data compression, computer graphics, and machine learning. Cluster analysis itself is not a specific algorithm, but the general task to be solved usually needs to modify the data preprocessing and model parameters until the results get the required attributes.

Figure 3. Cluster analysis.

• RMSD calculations

The root-mean-square deviation (RMSD) of atomic positions is a measure of the average distance between superposed protein atoms (usually backbone atoms). The RMSD calculation can also be applied to non-protein molecules, such as small organic molecules. When studying the conformation of globular proteins, usually after the best rigid bodies are superimposed, the similarity of the three-dimensional structure is measured by the RMSD of the Cα atomic coordinates.

Figure 4. RMSD.

• RMSF calculations

The root mean square fluctuation (RMSF) is used to describe the average size of the positional fluctuation of a particle group within a certain period of time. In terms of physical meaning, RMSD and RMSF both describe the deviation of the target state of the particle from the reference state. RMSD and RMSF analysis are collectively called the RMS analysis.

Figure 5. RMSF.

Services items

CD ComputaBio provides corresponding molecular dynamics simulation analysis services. Our molecular dynamics simulations analysis service provides accurate approximations of the behavior of real molecules and have proven to be very useful for understanding the different stages of drug development. We can also analyze these results for you. If you are interested in our services, please contact us for more detailed information. If you have any needs in this regard, please feel free to contact us.