Molecular Dynamics Simulation Service

CD ComputaBio has extensive experience in the field of molecular dynamics simulation (MD) services. Over the years, our computational chemist have provided many simulation services to hundreds of pharmaceutical and biotechnology companies. MD simulation is a set of molecular simulation methods, which is a powerful tool for studying the interaction of biological macromolecules and chemical compounds, and condensed matter systems. Through molecular dynamics simulation, researchers can obtain the motion trajectory of the atoms in the system and observe various microscopic details of the atomic motion process. Through the dynamic simulation of the research system, we can understand the movement and biological functions of biological macromolecules, the interaction mechanism between protein and small molecules, and the self-assembly process of nanomaterial molecules at the molecular level. Molecular dynamics simulation is a powerful supplement to theoretical calculations and experimental methods, and is widely used in the fields of physics, chemistry, materials science, and biomedicine.

Principle of MD

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Under the premise of ignoring the quantum effect of atomic nuclei and the adiabatic approximation of Born-Oppenheimer, molecular dynamics relies on Newtonian mechanics to simulate the motion of molecular systems, and samples are drawn from systems composed of different states of molecular systems, calculate the thermodynamic quantities and other macroscopic properties of the system. In molecular dynamics simulation, empirical potential is generally used to replace the interaction potential between atoms, such as Lennard-Jones potential, Mores potential, EAM atom insertion potential, F-S many-body potential.

Process of molecular dynamics simulation

Structure preparation, including structural processing of biological macromolecules and small molecules, coenzymes and solvent molecules;
Perform kinetic simulations, including energy optimization, heating, equilibrium phase and production phase;
Analyze the trajectory, including RMSD/RMSF, hydrogen bond analysis, cluster analysis, PCA, and binding free energy calculation.

Figure 1. Process of molecular dynamics simulations.

Principle of MD

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CD ComputaBio currently has molecular dynamics software such as AMBER, GROMACS and NAMD. Relying on the platform's computing resources, it can perform dynamic simulations with a time span of 100ns in a short time. By analyzing the clustering of the simulated trajectory, the relatively stable configuration of each state between the molecules can be obtained, and the mechanism of the interaction between the molecules can be identified by analyzing the interaction mode and the interaction energy between the molecules.

AI-based approaches

AI-based molecular dynamics simulation can be used to understand and predict protein sequences, which can solve the folding problem in the prediction process.
AI-based molecular dynamics simulation can be used to study the heat transfer of carbon nanotubes (CNT). First, MD simulation is used to analyze the influence of size, chirality and vacancy defects on the thermal conductivity of CNTs. Then the data obtained using MD simulation is input into the AI cluster, and the performance of the proposed model is evaluated relative to the actual results. The MD-based AI model can simulate the thermal conductivity of CNTs well, and can then be used to supplement the analysis solutions developed by MD simulation.

Service items

Project name	Molecular Dynamics Simulation Service
Advantages	Dynamic research methods. Rich analytical tools. It can be seamlessly combined with molecular docking, pharmacophore and other molecular simulation methods.
Services	Interaction between macromolecules and small molecules (interactions between drugs and targets). Interaction between macromolecules (protein-protein interaction) Solvent and solute interaction. The relationship between optimized structure and function and properties of three-dimensional structure of macromolecules and small molecules. Self-assembly simulation.
Cycle	Depends on the time you need to simulate and the time required for the system to reach equilibrium.
Product delivery mode	The simulation results provide you with the raw data and analysis results of molecular dynamics.
Price	Inquiry

Optional analysis items

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Molecular conformation sampling (cluster analysis, dominant conformation recognition).
Interaction analysis (hydrogen bond network, Contact-Map).
Binding free energy calculation (MM-PBSA, TI, FEP).
Skeleton fluctuation analysis (RMSD, RMSF).
Hot residue analysis (Alanine-scanning, Energy-decomposition).
Conformational transformation analysis (PCA, Energy-landscape plotting).
Analysis of physical and chemical properties (energy, volume, pressure, temperature, density monitoring).

Why choose us?

Our team has extensive experience in molecular dynamics simulation of drugs and biological systems.
We have independently or assisted customers to complete a large number of related topics, and many of our results have been published in various well-known SCI journals.
Our researchers can quickly understand the situation of the project through simple descriptions, and quickly establish a feasible research plan according to the needs of the client, saving a lot of literature research time.
In addition, we cooperate with a number of universities or research institutions, and can consult industry experts for their opinions and suggestions on some complex issues.

Reference:

Vijayaraghavan V , Garg A , Wong C H , et al. A molecular dynamics based artificial intelligence approach for characterizing thermal transport in nanoscale material. Thermochimica Acta, 2014, 594:39-49.
Zachary Smith, et al. Discovering Protein Conformational Flexibility through ArtificialIntelligence-Aided Molecular Dynamics. The Journal of physical chemistry B. 2020, 124, 8221−8229