Service

MD Simulation

Physics-based molecular dynamics simulation service that validates docking hypotheses by measuring stability,
flexibility, and interaction persistence over time under realistic solvent conditions.

What we deliver

Trajectory package + key stability metrics (RMSD/RMSF/contacts)
Interaction persistence and binding-mode integrity summary
Go/No-Go recommendation for experimental follow-up

Best for

Validating top docking hits before wet-lab
Removing “looks good but unstable” candidates
Comparing variants, mutants, or formulation scenarios

RMSD distribution
Conformer/pose stability signal used to detect drift and unstable binding modes.

Contacts persistence within 10 Å (boxplot)

Contact persistence (10Å)
Contact count distribution over time; supports persistence-based ranking across candidates.

Run dashboard (animation)
Trajectory-driven monitoring view that summarizes time evolution and key metrics.

Scope

Protein–ligand MD

Pose stability over time
Contact persistence and water-mediated interactions
Stability ranking across candidates

Protein–protein / peptide MD

Interface integrity and contact networks
Hotspot residue stability
Mechanism-aligned interpretation

Workflow

MD is used as the validation gate after docking. Outputs are curated for decision-making rather than raw logs.

System setup

Solvation, ions, force-field selection, constraints.

Equilibration

Stabilize system before production dynamics.

Production run

Collect trajectories for stability assessment.

Analysis & decision

RMSD/RMSF/contacts + shortlist recommendation.

Stability gate

RMSD distribution supports identifying stable vs drifting poses.

Persistence gate

Contact persistence within a cutoff distance supports interaction robustness scoring.

Operational trace

Dashboard view provides a quick read of run status and metric evolution.

Deliverables

Files

Trajectories (DCD/XTС) + structures (PDB)
Key metrics (CSV): RMSD, RMSF, contacts
Summary report (PDF/MD)

Interpretation

Binding-mode integrity assessment
Interaction persistence highlights
Go/No-Go recommendation rationale

Inquire (BD)
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