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Molecular Dynamics Simulation Service

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Molecular Dynamics Simulation Service

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Molecular Dynamics Simulation Service for Docking Validation, Binding Free Energy & Lead Optimization

Validate docking poses, assess protein-ligand complex stability, estimate binding free energy and prioritize compounds, variants or biologics candidates using customized MD simulation workflows.

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Docking pose validation Protein-ligand stability MM-PBSA / MM-GBSA / FEP Mutation effect analysis

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100 ns–μs Simulation Scale

Flexible simulation lengths for stability and dynamics analysis.

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10+ Analysis Metrics

RMSD, RMSF, H-bonds, contacts, SASA, clustering, PCA, and free-energy estimation.

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1 Decision-Ready Report

Clear conclusions for pose validation, candidate ranking, and next-step planning.

Post-Docking MD Simulation for Hit Prioritization

See how MD simulation supports docking pose validation, protein-ligand stability analysis and candidate prioritization before experiments.

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Need a similar workflow?

Send a brief note and our scientists can suggest a suitable MD workflow.

What MD simulation helps your team decide

Docking validation

Is the predicted pose stable?

Assess whether a docked ligand, peptide or complex remains stable under simulated dynamic conditions.

Lead prioritization

Which hit should be tested next?

Compare stability, interaction persistence, conformational behavior and free-energy estimates across candidate compounds.

Engineering support

Which mutation changes stability or binding?

Compare wild-type and mutant systems to prioritize protein engineering, antibody or enzyme optimization experiments.

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Comparison of MD Methods

Application Scenario / Project Need	Recommended MD Method	Large / Long Systems	Enhanced Sampling	Typical Output
Docking pose validation Protein-ligand stability check Mutation effect analysis	All-Atom MD Simulations	Limited	—	RMSD/RMSF, H-bonds, contact persistence, representative structures
Membrane protein dynamics Large biomolecular assemblies Long-timescale motion trends	Coarse-grained Dynamics Simulations Service	✓	—	Global motion, assembly behavior, membrane dynamics, mesoscale trends
Ligand unbinding pathway Conformational transition analysis Energy barrier estimation	Umbrella Sampling Simulation Service	Project-dependent	✓	PMF profile, energy barrier estimate, preferred transition pathway
Forced ligand dissociation Binding pocket exit-route exploration Rupture event analysis	Steered Molecular Dynamics	Project-dependent	✓	Pulling pathway, force response, interaction-breaking events
Flexible peptide sampling Loop motion analysis High-barrier state exploration	Replica Exchange Molecular Dynamics (REMD)	Limited	✓	Conformational ensemble, state populations, improved sampling results
Open-to-closed transition Domain motion analysis Known start-to-target pathway	Targeted Molecular Dynamics (TMD) Simulation	Project-dependent	Guided	Transition pathway, intermediate conformations, structural motion map

Choose a method based on: project question, system size, required resolution, sampling difficulty, available structures, expected deliverables, budget and timeline.

Choose the Right MD Method for My Project

Project workflow

Project intake and endpoint definition

Define whether the project is for docking validation, hit ranking, free-energy analysis, mutation effect, antibody interface stability or membrane protein dynamics.

System preparation

Prepare protein/ligand structures, force fields, protonation states, cofactors, ions, membranes and solvent models based on project requirements.

Equilibration and production MD

Run suitable nanosecond-to-microsecond workflows depending on biological question, budget and precision requirements.

Trajectory and interaction analysis

Analyze RMSD, RMSF, radius of gyration, hydrogen bonds, hydrophobic interactions, salt bridges, clustering and representative conformations.

Free-energy and comparative assessment

Apply MM-PBSA, MM-GBSA, FEP, umbrella sampling or PMF methods when appropriate to support ranking and mechanistic interpretation.

Report and next-step recommendation

Deliver files, figures and an actionable recommendation for synthesis, assay, redesign, mutation testing or further simulation.

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Inputs required

PDB / AlphaFold model / prepared docking pose
Ligand SMILES, SDF, MOL2 or compound library files
Known binding site, reference ligand, assay data or SAR if available
Mutation list, antibody-antigen complex, membrane context or cofactors if relevant
Decision objective: validate pose, rank hits, evaluate mutation, estimate binding free energy

Deliverables

Simulation trajectories and representative conformations
RMSD, RMSF, radius of gyration and clustering analysis
H-bond, hydrophobic, salt-bridge and interaction persistence analysis
MM-PBSA / MM-GBSA / FEP or other free-energy outputs when appropriate
2D/3D visualizations and technical report
Prioritized recommendation for next experiment or optimization step

Check My Input Data

Representative project examples

Docking hit validation

Goal: choose 10 compounds from 50 docked hits.
Workflow: short MD → pose stability → contact persistence → hit ranking report.

Lead optimization with free energy

Goal: compare analog series.
Workflow: prepared complexes → MD/FEP or MM-GBSA → SAR-informed prioritization.

Antibody-antigen interface stability

Goal: evaluate variant impact.
Workflow: WT/mutant MD → interface contacts → stability and mutation recommendation.

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FAQ

Why is MD simulation useful after docking?

Docking gives a static pose. MD simulation evaluates whether that pose remains stable under dynamic conditions and whether key interactions persist over time.

Which free-energy method should I choose?

MM-PBSA/MM-GBSA are often used for practical comparative ranking; FEP can be used for more rigorous lead optimization when a suitable congeneric series and data context are available. The best method depends on project objective, input quality and budget.

Can you run MD for antibody-antigen or protein-protein complexes?

Yes. MD can be used to analyze interface stability, contact persistence, conformational flexibility and mutation effects in macromolecular complexes.

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