Molecular Dynamics Simulations

The molecular dynamics (MD) method is based on molecular force fields, which can dynamically describe the motion of molecules and thus the dynamic processes of life. It has a wide range of applications in the life sciences, such as the study of protein folding mechanisms, the study of enzyme-catalyzed reaction mechanisms, and the study of large-scale conformational changes in biological macromolecules.

Our company provides customized professional MD simulation services for our customers' innovative scientific research, applying low-energy conformational modeling of macromolecular systems, X-ray crystal diffraction, and processing of NMR experimental results. We evaluate each project individually before providing analytical advice and fees.

Service Overview

Our company currently has MD software such as AMBER, GROMACS and NAMD. Relying on the computational resources of this platform, dynamic simulations with a time span of 100 ns can be performed in a short period of time. By analyzing the clustering of simulated trajectories, the relatively stable conformation of each state between molecules can be obtained. In addition, by analyzing the mode of interaction and interaction energy between molecules, the mechanism of interaction between molecules can be determined.

Our MD simulation service is particularly useful in computer-aided drug discovery. It can be used to identify hidden or xenobiotic binding sites, enhance traditional virtual screening methods, and directly predict the binding energies of small molecules.

Specific services include:

• Material adsorption studies.
• Protein-protein interaction studies.
• Studying the interactions between large and small molecules.
• Predicting the interaction between drug molecules and proteins/DNA.
• Relationship studies between structure, function and properties.
• Optimization of 3D structures of molecules (drug, protein, material molecules), such as homology modeling of optimized structures.

Service Process

The general workflow of Our company's MD simulation service follows these steps.

• Step 1: A model system is selected where the missing fragments are fixed and the protonation state is determined.
• Step 2: Minimize and equilibrate the energy of the system by solving the Newtonian equations of motion until the properties of the system no longer change with time.
• Step 3: After equilibrium, a production run is performed for an appropriate time period, the trajectory is output, and the properties of interest are then analyzed.

Research Capabilities

Our company uses MD simulation methods to help clients predict changes in protein systems over time. Protein systems can contain proteins, DNA/RNA, lipids and other small ligands so that events of biological and pharmaceutical significance can be explored. Specifically, simulations can be used to characterize protein flexibility, refine experimentally determined structures, evaluate protein-ligand binding, and even monitor protein folding processes.

Fig.1 Molecular dynamics simulation for rational protein engineering. (Rouhani M, et al. 2018)

If you are looking for smarter, higher quality solutions that incorporate best practices, please feel free to contact us.

Reference

1. Rouhani M, et al. (2018). "Molecular Dynamics Simulation for Rational Protein Engineering: Present and Future Prospectus." Journal of Molecular Graphics and Modelling. 84: 43-53.

It should be noted that our service is only used for research, not for clinical use.