Molecular Dynamics Simulation

Molecular Dynamics ( MD ) simulation is a rapidly developing molecular simulation method in recent years. It is based on classical mechanics, quantum mechanics and statistical mechanics, and uses computer numerical method to solve the motion equation of molecular system.As the third scientific method to study molecular structure and properties, molecular dynamics simulation has been widely used in chemical engineering, material science and engineering, physics, biological medicine and other fields of science and technology.This technique can not only obtain the trajectory of atoms, but also observe various microscopic details in the process of atomic motion.It is a powerful supplement to theoretical calculations and experiments, and the main advantages include the dynamic of the research method, abundant analytical means, and seamless combination with molecular docking and pharmacophore and other molecular simulation methods.

A schematic example from Wecomput MD simulation report (investigating the conformational transition process of a certain structure)

【Research Content of Molecular Dynamics Simulation】

  • Self-assembly simulation
  • Interaction between macromolecules and small molecules (drug-target interaction)
  • Interaction between macromolecules (protein-protein interaction)
  • Interaction between solvent and solute
  • Optimization of 3D structure of macromolecules and small molecules
  • The relationship between structure, function and properties

【Optional Analysis Items】

  • Molecular conformation sampling (cluster analysis, dominant conformation recognition)
  • Interaction analysis (hydrogen bond network, contact map)
  • Binding free energy compute (MM-PBSA, Ti, FEP)
  • Skeleton fluctuation analysis (RMSD, RMSF)
  • Hot spot residues analysis (Alanine-scanning, Energy-decomposition)
  • Conformational transition analysis (PCA、Energy-landscape plotting)
  • Physicochemical properties analysis (energy, volume, pressure, temperature, density monitoring)

【Service features and advantages】

Wecomput is a professional information science company providing the overall solution of molecular dynamics simulation service. Our team members are researchers from famous universities or scientific research institutions at home and abroad, and have rich experience in molecular dynamics simulation of drugs and biological systems.We have completed a large number of related projects independently or assisted our clients. With experiments and compute complementing each other, many results have been published in various SCI journals. Our researchers have a full understanding of biological experiments. We can quickly understand the situation of the project, and according to the needs of the client, quickly establish a set of feasible research scheme, saving a lot of time of literature research. In addition, we have cooperation with many universities or research institutions, and we can consult experts in the industry for their opinions and suggestions on some complex issues. After all the computes are completed, we can issue Chinese and English analysis reports according to the requirements of the client, assist in writing English academic papers or patents, and provide contribution suggestions.