Molecular Dynamics Simulation
Molecular dynamics (MD) as a part of structure-based drug design plays a crucial role in modern drug discovery by providing insights into the behavior and interactions of biomolecules at the molecular level. By solving Newton's equations of motion, MD generates trajectories for all atoms in the system, enabling the computation of various properties. As a result, this vital data is used for designing and optimizing drug candidates with high specificity and efficacy.
Here at Chemspace, we offer a wide range of MD simulation services applicable to the proteins
and the protein-ligand complexes to give important insights into the dynamics and function of
the targets and facilitate the evaluation of the binding energetics and kinetics of the
ligand-receptor interactions, therefore guiding the choice of the best candidate molecules
for further development.
Simple Protein MD Simulation Studies
By simulating the movement and behavior of atoms within a protein structure we offer:
- Finding the correct conformation and estimation of conformation stability;
- 4D structures: building the ensemble of pocket conformations for molecular docking;
- Assessing side chain modality.
MD for investigating Ligand Binding
We offer:
- Steered MD. This method can be used as a rapid postprocessing tool for discriminating active and inactive binders by simply analyzing the SMD-derived force profiles related to ligand unbinding simulations [1].
- Absolute and relative binding free energy (A/RBFE). By using AToM-OpenMM software binding free energies can be accurately computed thus boosting lead optimization in structure-based drug discovery [2].