Molecular Dynamics Simulations Service

Molecular Dynamics (MD) is one of the most commonly used methods in molecular simulation. Based on molecular force fields, this method is able to dynamically describe the motion of molecules and subsequently the dynamic processes of life. Molecular dynamics simulations can help you understand the motion and biological functions of biological macromolecules and protein-small molecule interactions at the molecular level.

Molecular dynamics (MD) simulation (Lazim et al., 2020)

Molecular dynamics has a wide range of applications in the life sciences, such as the mechanistic study of protein folding, the mechanistic study of enzyme-catalyzed reactions, the study of the motion of functionally relevant proteins, and the study of large scale conformational changes of biological macromolecules. Currently, molecular dynamics methods have been successfully applied to the modeling of low-energy conformations of macromolecular systems, X-ray crystal diffraction, and the processing of NMR experimental results. This technique can be seamlessly integrated with molecular simulation methods such as molecular docking and pharmacophore.

Creative Proteomics offers molecular dynamics simulation services. We can provide you with services including but not limited to:

• Study of macromolecule-small molecule interactions, e.g., prediction of drug molecule-protein/DNA interactions, material adsorption, etc.
• Study of macromolecular interactions (protein-protein interactions)
• Study of interaction mechanisms in ligand-receptor complex systems: interaction modes, induced fit effects, protein backbone motion
• Predicting the binding free energy of active small molecules (and thus Ki, IC50), elucidating mechanisms or guiding structural modifications.
• Optimization of three-dimensional structures of molecules (drugs, proteins, material molecules), such as optimization of homologous modelling
• Study of the relationship between structure and function and properties

Optional Analysis Projects

• Molecular conformation sampling (cluster analysis, dominant conformation identification)
• Interaction analysis (hydrogen bonding network, Contact-Map)
• Binding free energy calculations (MM-PBSA, TI, FEP)
• Backbone fluctuation analysis (RMSD, RMSF)
• Hot spot residue analysis (Alanine-scanning, Energy-decomposition)
• Conformational transition analysis (clustering, PCA, simple normal mode analysis, secondary structure analysis, potential energy surface scanning, dominant conformation identification)
• Physico-chemical property analysis (energy, volume, pressure, temperature, density monitoring)

Main Processes of Molecular Dynamics Simulation

A. Structural preparation: structural treatment of biological macromolecules and small molecules as well as coenzymes, solvent molecules, etc.

B. Kinetic simulations: energy optimization, heating, equilibrium phase and production phase

C. Analytical trajectories: RMSD/RMSF, hydrogen bonding analysis, cluster analysis, PCA, binding free energy calculations

Deliverables

• Provide molecular dynamics model
• Specific experimental procedure (experimental steps; description of main instruments and reagents)
• Analysis of raw data and related results

Creative Proteomics has considerable practical experience and core technologies in molecular docking research, providing efficient and high-quality technical services to a wide range of researchers. If you have questions or other needs, please contact us.