Molecular
Dynamics
Simulations
High-quality MD simulations that reveal how your proteins move, bind, and interact — delivered by expert bioinformaticians in 24–48 hours, since 2020.
What We Can Do For You
Submit your structure files — we handle system preparation, solvation, force-field selection, equilibration, and analysis. You define the science; we deliver the simulation.
Protein–Ligand Complexes
Understand how small-molecule drugs, inhibitors, or cofactors bind and behave within a protein binding pocket over time — essential for drug discovery and lead-optimisation workflows.
Protein–Protein Complexes
Explore the dynamics of protein–protein interactions, including antibody–antigen binding, receptor–ligand signalling, and multi-chain assemblies at the atomistic level.
Mutant & Engineered Proteins
Characterise the structural consequences of point mutations, insertions, or deletions — compare wild-type vs mutant dynamics and assess thermodynamic stability changes.
Research Areas We Support
From hit-to-lead drug discovery to de novo protein engineering — our MD simulations are tailored to your specific research goal.
Drug Discovery
MD-guided hit identification and binding mode validation for novel therapeutic targets — bridging docking predictions with simulation-confirmed stability.
Lead Optimisation
Compare chemical analogues in simulation to guide SAR decisions — identify which modifications improve binding affinity, selectivity, and stability.
Enzyme Engineering
Characterise engineered enzyme variants at the atomistic level — validate activity, thermostability, and substrate accommodation before wet-lab synthesis.
In Silico Mutagenesis
Computationally mutate key residues and assess the structural, dynamic, and thermodynamic consequences — prioritise mutations before experimental testing.
Site-Directed Structural Optimization
Refine binding site geometry to improve drug–target complementarity — simulate redesigned pockets and evaluate conformational changes under realistic conditions.
Ligand Modifications & Enhancement
Evaluate scaffold modifications — functional group additions, ring substitutions, linker changes — and their effect on binding mode and residence time.
Bespoke Workflows Available
Have a use case not listed above? We design custom MD protocols for any protein system or research goal — get in touch before ordering.
Discuss your project
De Novo Protein Design
Validate computationally designed or AI-generated protein folds via MD — confirm structural stability, dynamics, and functional conformation in explicit solvent.
De Novo Ligand Design
Screen and validate novel ligand scaffolds in silico against your target — assess binding geometry, stability, and pharmacophore fit before synthesis.
Analysis Capabilities
Every simulation includes standard structural analyses. Add specialist analyses at checkout — or ask us and we'll recommend the right combination for your research goals.
From Structure to Molecular Dynamics Insights in 3 Steps
Submit Your Structure & Parameters
Upload your protein file (PDB, MOL2, or zip), specify your simulation engine, duration, and the number of complexes. You can also provide your own topology files, force-field parameters, custom restraints, or any specific run settings — our team will incorporate them exactly.
We Prepare & Run the Simulation
Our team solvates the system, assigns force-field parameters, minimises energy, equilibrates under NVT/NPT ensembles, and then runs your full production MD simulation on dedicated high-performance compute resources.
Receive Results Within 24–48 Hours
You receive trajectory files, a full suite of analysis plots, and a detailed written report — all formatted for publication or direct inclusion in grant applications.
Five Simulation Engines, One Team
Choose the platform that suits your workflow, or describe your needs and we'll recommend the best engine for your specific protein system, force field, and analysis goals.
GPU-accelerated engine from Schrödinger, renowned for accuracy in protein–ligand sampling and free-energy perturbation.
- OPLS4 force field support
- FEP+ compatible
- Seamless Maestro visualisation
The world's most widely used open-source MD package — exceptional performance for biomolecular simulations.
- AMBER, CHARMM, GROMOS force fields
- Optimised for CPUs & GPUs
- Rich post-processing ecosystem
Python-native MD toolkit with state-of-the-art GPU acceleration, ideal for custom force fields and machine learning potentials.
- ML/AI force-field ready
- Highly scriptable in Python
- Polarisable force fields
Developed at UIUC, NAMD excels in large-scale biomolecular simulations across CPUs, GPUs, and supercomputer clusters.
- CHARMM & AMBER force fields
- Massively parallel scalability
- Membrane & lipid bilayer systems
Industry-standard for nucleic acids and proteins alike — AMBER force fields set the benchmark for biomolecular simulations.
- FF14SB, GAFF2 force fields
- Excellent nucleic acid support
- Free-energy methods (TI, FEP)
Publication-Ready Analysis Figures
Every order ships with a complete suite of analysis plots. Hover any card to learn what each analysis tells you about your protein system.
RMSD
Root-mean-square deviation of the backbone over time — shows when your protein equilibrates and how stable it remains.
RMSF
Per-residue flexibility profile — reveals which loops, termini, or binding-site residues are most mobile during the simulation.
Ligand RMSD
Tracks the ligand's position within the binding pocket over time — a flat line confirms stable binding throughout the simulation.
Radius of Gyration
Measures how compact the protein remains throughout the simulation — a stable RGyr confirms the protein does not unfold.
SASA
Solvent-accessible surface area tracks protein exposure to solvent — useful for studying burial of hydrophobic residues upon binding.
Polar Surface Area
Monitors how polar surface area changes during the simulation — correlates with drug permeability and binding-mode stability.
MM-GBSA / PBSA
Per-frame binding free energy estimation — quantifies how strongly your ligand binds and which residues contribute most to affinity.
PCA
Principal Component Analysis maps the conformational space sampled — each cluster represents a distinct protein state visited during the simulation.
DCCM
Dynamic Cross-Correlation Matrix reveals which pairs of residues move together — essential for identifying allosteric communication networks.
Everything You Need for Publication
- Full Trajectory Files Standard formats (XTC, TRR, DCD) compatible with VMD, PyMOL, GROMACS tools, or any downstream analysis pipeline.
- RMSD, RMSF & Ligand RMSD Plots Backbone stability, per-residue flexibility, and ligand positional drift — confirming whether binding is maintained throughout.
- Radius of Gyration & SASA Compactness and solvent exposure metrics confirming correct folding and stability in solution throughout the simulation.
- H-Bond & Key Contact Analysis Protein–ligand hydrogen-bond occupancy throughout the trajectory — identifies residues driving binding specificity.
- PCA & MM-GBSA — Optional Add-ons Conformational clustering (PCA) and binding free-energy estimation (MM-GBSA/PBSA) — +$5 USD each, select at checkout.
- Detailed Scientific Write-Up A structured report interpreting all results in the context of your research question — formatted for manuscripts or grant applications.
Guaranteed Delivery
From Your Protein to Publication-Ready Results
Here's exactly what happens when you order — using a SARS-CoV-2 main protease (Mpro) inhibitor study as an example.
View full case study — SARS-CoV-2 Mpro + N3 Inhibitor
Pipeline
The BioCode Advantage
Guaranteed Turnaround
Results in days, not weeks — our dedicated compute infrastructure ensures your project never waits in a queue. Delivery time guaranteed at the point of order.
Simulations Completed
Over 10,000 simulations delivered across 6 years of professional service. Every order includes a pre-simulation consultation — we work with you to fully understand your research goals before we begin.
Order Your MD Simulation
Configure your simulation below, get an instant price, and upload your protein files — all in one form. Our team will confirm your order and begin within hours.
