Molecular Dynamics (MD) Simulation

Molecular Dynamics (MD) Simulation

Molecular dynamics (MD) simulation is a powerful tool to study the dynamic behavior of biomolecules such as proteins and DNA. The technique can help in the mechanism of action of biomolecules in performing physiological functions, and identification of small molecules with potential targets by simulating the state of motion of biomolecules in three-dimensional space. In addition, it can simulate complete atomic detail and very fine temporal resolution, as well as capture the behavior of proteins and other biomolecules, which is important for protein engineering and drug discovery.

CD BioSciences has biophysical technology platforms such as X-ray crystallography, electron microscopy, and nuclear magnetic resonance (NMR) to capture a wide range of important biomolecular processes including conformational changes, ligand binding, and protein folding, revealing the location of all atoms with femtosecond time resolution.

application of molecular dynamics (MD) simulationFigure 1. MD simulation of MnAs-ICG nanospike. (Xu X, et al., 2023)

Applications in Molecular Dynamics (MD) Simulation

CD BioSciences combines computers with molecular dynamics research, utilizing advanced biophysical techniques in the study of proteins, drugs, biofilms, and more, to reveal the most precise interactions between molecules.

Protein Analysis

Protein disorganization and aggregation play an important role in the pathogenesis of many neurodegenerative diseases such as Alzheimer's disease and Parkinson's disease. The end product of the aggregation process in these diseases is highly structured amyloidogenic fibrils. Therefore, we provide MD simulation technology to give comprehensive technical support for the rational design of drugs for amyloid oligomer formation. Our technology simulates the dynamics of proteins in physiological environments, including protein folding, unfolding, stabilization, and interactions with other molecules, to provide clients with a better understanding of the physicochemical forces driving protein aggregation. In addition, we provide high temporal and spatial resolution systems imaging techniques to capture the key steps in the formation of amyloid oligomers.

Drug Research

We can provide biophysical techniques such as X-ray crystallography, electron microscopy, and nuclear magnetic resonance (NMR) to study the binding modes and mechanisms of action of drugs with specific target molecules in biological systems, which are important for drug design and discovery. Meanwhile, using MD simulations, we can calculate binding energies to verify the effective binding of proteins to screened small molecule ligands. In addition, we can study the mechanism of drug-target protein interaction, which provides direct clues for drug design and new drug discovery.

Biofilm Research

Biofilms have a variety of biological functions, such as protecting cells, regulating the entry and exit of selected substances, recognizing specific substances, and receiving physicochemical biological information at certain biochemical reaction sites. We combine computers to apply MD simulation techniques to model the structure of biofilms, their dynamics, and their interactions with proteins, thus revealing the role of biofilms in cellular signaling and substance transport processes.

Accuracy Testing of Modeled Structures

Our service platform provides biophysical techniques such as X-ray crystallography and fluorescence imaging for generating high-resolution structural data and 3D structural images of biomolecules. Since crystal structures may be affected by lattice stacking or, in the case of membrane proteins, artifacts may appear due to the lack of a lipid bilayer. Our MD simulation techniques can often correct such artifacts by starting the simulation from the crystal structure in a suitable solvent environment and allowing the structure to relax to a more favorable conformation.

Advantages of Our Services

  • Strong technical support. Our service platform covers a wide range of biophysical analysis techniques aimed at offering comprehensive support to our clients.
  • Rich experience reserves. With the most advanced equipment and the most professional team of biophysicists, we are able to provide accurate experimental data.
  • Individualized solutions. To satisfy the needs and requirements of different clients, we will arrange for experts to develop a reasonable and customized service process.

Related Services

CD BioSciences has a comprehensive biophysical technology platform, which is focused on the study of conformational changes and arrangements of biomolecules to reveal the mechanisms involved in the execution of their physiological functions. If you are interested in our services, please contact us.


  1. Xu X, Liu A, Liu S, et al. (2023). Application of molecular dynamics simulation in self-assembled cancer nanomedicine[J]. Biomaterials Research. 27(1): 39.
For research use only, not intended for any clinical use.
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CD BioSciences is a biotechnology company focused on biophysical services. We are proficient in both chemistry and biophysics, and have a comprehensive biophysical platform containing a wide range of advanced technologies.

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