ICDMO provides molecular dynamics (MD) simulation for protein complexes and protein–small molecule interactions. MD simulation uses 3D structures (PDB format) as initial models with classical force fields to describe atomic interactions, dynamically tracking atom trajectories to reveal binding and dissociation processes, interface rearrangement, conformational transitions, and key residue contributions to stability. Simulations are performed on in-house HPC servers for fast turnaround and fully reproducible results — all integrated with downstream experimental validation platforms (Y2H, Co-IP, SPR, MST, BLI, ITC).
AMBER ff14SB force field is applied for protein atoms; AmberTools antechamber with AM1-BCC charges is used for small molecules. Systems are solvated in a TIP3P explicit water box (10 Å buffer), neutralized with Na⁺/Cl⁻ ions, and subjected to energy minimization → heating (0 K → 300 K, Langevin thermostat) → NPT density equilibration → unrestrained production MD (50–400 ns, trajectory output every 10 ps). Trajectory analysis uses cpptraj (AMBER) and VMD visualization.
Note: All services are for research use only and not intended for diagnostic or therapeutic purposes.
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