Molecular Dynamics Simulations

Creative Biostructure provides molecular dynamics (MD) simulations service, your gateway to unlocking the intricate world of biomolecular interactions and dynamics. Our cutting-edge service is designed to delve into the fundamental essence of life - the molecular intricacies that govern the behavior of proteins, nucleic acids, and other biomolecules.

What Are Molecular Dynamics Simulations?

MD simulations are computational techniques that simulate the behavior of molecules over time. By tracking the positions and velocities of individual atoms within a system, we gain invaluable insights into how these molecules interact, fold, and function. This is particularly significant in structural biology and biophysics, as it allows us to bridge the gap between static crystallographic structures and dynamic biological processes.

It is based on classical mechanics, quantum mechanics, and statistical mechanics. It uses computer numerical methods to solve the equation of motion of molecular systems to simulate and study the structure and properties of molecular systems. This technology can not only obtain the motion trajectory of atoms but also observe various microscopic details in the process of atomic motion. It is a powerful complement to theoretical calculations and experiments. It has the main advantages of dynamic research methods, rich analysis methods, and seamless integration with molecular simulation methods such as molecular docking and pharmacophore.

Our Workflow for MD Simulations

The main steps of a MD simulation include:

• Determine the Starting Configuration

A low-energy, structurally sound starting 3D configuration is the first step in performing MD simulations. we also provide protein modeling services.

• Selection of Appropriate Force Field and Simulation Software

Choosing an appropriate force field is the basis for MD simulations. Different force fields have different scopes of application and limitations and need to be properly selected according to the system and problems studied. The choice of software is often related to the force field used, and the required algorithm, operating speed, and parallel computing capability of the software should be considered emphatically.

• System Construction and Energy Minimization

There are often local irrationalities in the initially established system (such as the distance between adjacent atoms being too close), and the dynamic simulation cannot be performed immediately, and the energy minimization of the system needs to be carried out first.

• Balancing Process

In this process, it is necessary to monitor the energy, temperature, pressure, density, etc., of the system to see if it converges until the system reaches equilibrium.

• Data Collection Process

After the system reaches equilibrium, long-term simulations can be carried out, and samples are collected from this process for analysis. The simulation time should be as long as possible to ensure that the phenomenon or property under study can be observed, and it is necessary to ensure the repeatability of this phenomenon.

• MD Result Analysis

Comprehensive analysis of collected data and delivery of results.

Figure 1. The molecular dynamics simulation process.

What Can We Offer?

The analysis content of the commonly used MD simulations includes:

• Molecular Conformation: cluster analysis, dominant conformation identification
• Interaction Analysis: Hydrogen Bond Network, Contact-Map
• Binding Free Energy Calculations: MM-PBSA, TI, FEP
• Skeleton Fluctuation Analysis: RMSD, RMSF
• Hot Residue Analysis: Alanine-scanning, Energy-decomposition
• Conformational Transition Analysis: PCA, Energy-landscape plotting
• Analysis of Physical and Chemical Properties: energy, volume, pressure, temperature, density monitoring

MD simulations can be combined with other techniques to broaden its application spectrum:

• Quantum Mechanics: For more precise understanding of chemical reactions.
• Cryo-Electron Microscopy: To validate simulated structures.
• NMR Spectroscopy: To refine structures with experimental data.

Highlights of Our MD Simulations Service

• Expertise: Our team comprises experts with years of experience in MD simulations, ensuring the highest quality results and insightful data interpretation.
• Cutting-Edge Technology: We leverage the latest software and hardware, guaranteeing accurate and efficient simulations.
• Customization: Our service is highly customizable, catering to your specific project requirements.
• Comprehensive Support: We're not just a service provider; we're your research partner. We offer guidance, consultations, and assistance throughout your project.
• Timely Delivery: Our commitment to punctuality ensures that your research progresses without unnecessary delays.

Creative Biostructure has rich experience in molecular dynamics simulations research. Whether you're delving into protein dynamics, drug discovery, or material design, we provide tailored solutions to accelerate your scientific endeavors. Please feel free to contact us, and we will be your trusted partner.

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References

1. Badar M S, et al. Molecular dynamics simulations: concept, methods, and applications. Transdisciplinarity. Cham: Springer International Publishing, 2022: 131-151.
2. Hu X, et al. Molecular dynamics simulation of the interaction of food proteins with small molecules. Food Chemistry. 2022: 134824.