Molecular Dynamics Simulation Service
Molecular dynamics (MD) is a computer simulation that analyzes the physical motion of atoms and molecules. The dynamics of the system can be seen by allowing atoms and molecules to interact with each other for a fixed period. MD simulation analysis is one of the essential steps while designing novel drugs using computational approaches. Molecular dynamics simulation is a powerful supplement to theoretical calculations and experimental methods, and is widely used in the fields of physics, chemistry, material science, and biomedicine.
Our Service
Coarse-grained Dynamics Simulation
Intracellular interaction processes usually involve a large number of different types of biomolecules as well as collective motions of biomolecules, which usually last on the order of microseconds to milliseconds or more. Conventional all-atom simulations are difficult to realize. Therefore, We provide coarse-grained dynamics simulation service to reduce the degrees of freedom of the simulated system by simplifying the details of the full-atom simulation.
All-atom Molecular Dynamics (MD) Simulations
We provide the following services using all-atom dynamics simulations:
Investigate the interaction mechanisms of ligand-receptor complex systems: interaction modes, induction of fitting effects, protein backbone motions.
Prediction of binding free energies of active small molecules (correlation with Ki, IC50) to elucidate mechanisms or guide structural modifications.
Replica Exchange Molecular Dynamics (REMD)
We perform separate molecular dynamics simulations for each replica. Configurations of each replica with adjacent temperatures are interchangeable according to the Metropolis standard.
REMD simulations allow the low-temperature configuration space to escape the local potential energy minimum.
REMD simulations can sample a larger configuration space than conventional dynamics.
Up to 1000ns
Tools for Molecular Dynamics Simulations
AMBER
AMBER is a type of molecular dynamics simulation used to study the behavior and properties of organic molecules. This simulation is useful for predicting how molecules will interact with each other, as well as how they will respond to various external factors like temperature and pressure.
GROMACS
ROMACS is used to study the dynamics of complex biological macromolecules such as proteins, lipids and nucleic acids. It is designed to efficiently simulate the motion of macromolecules and can be used to simulate a variety of biological processes such as protein folding, membrane dynamics, and protein-ligand interactions.
NAMD
NAMD is a force field commonly used in molecular dynamics simulations to study the behavior of macromolecules such as DNA and proteins. The force field describes the interactions between atoms in a molecule and is used to predict the conformation (three-dimensional shape) and dynamics of the system.
Methods of Post-simulation Analysis
- RMSD (root-mean-square-deviation)
- Hydrogen Bond Analysis
- SASA (Solvent Accessible Surface Area)
- Principal Component Analysis (PCA)/ Dynamic Cross-Correlation Matrix Analysis (DCCM)
- RMSF (root-mean-square fluctuation)
- Radius of Gyration (Rg)
- Contact Frequency Analysis or Contact Area Analysis
- MMGBSA/MMPBSA Binding Free Energy (with its decomposition)
At CD ComputaBio, we offer cutting-edge molecular dynamics (MD) simulation services to accelerate the progress of scientific research and development. CD ComputaBio has rich practical experience and core technology in molecular docking research and can provide efficient and high-quality technical services for researchers. If you have questions or other needs, please contact us.
References:
- Ye H, Xian W, Li Y. Machine learning of coarse-grained models for organic molecules and polymers: Progress, opportunities, and challenges. ACS omega, 2021, 6(3): 1758-1772.
- Černý J, Božíková P, Balík A, et al. NMDA receptor opening and closing—transitions of a molecular machine revealed by molecular dynamics. Biomolecules, 2019, 9(10): 546.
- Qi R, Wei G, Ma B, et al. Replica exchange molecular dynamics: a practical application protocol with solutions to common problems and a peptide aggregation and self-assembly example. Peptide self-assembly: Methods and protocols, 2018: 101-119.
- Patel J S, Berteotti A, Ronsisvalle S, et al. Steered molecular dynamics simulations for studying protein–ligand interaction in cyclin-dependent kinase 5. Journal of chemical information and modeling, 2014, 54(2): 470-480.
- McCormick J W, Ammerman L, Chen G, et al. Transport of Alzheimer’s associated amyloid-β catalyzed by P-glycoprotein. PLoS One, 2021, 16(4): e0250371.
- You W, Tang Z, Chang C E A. Potential mean force from umbrella sampling simulations: What can we learn and what is missed?. Journal of chemical theory and computation, 2019, 15(4): 2433-2443.
* For Research Use Only.
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