Does the pose persist?
Is the starting arrangement maintained during the simulation, or does it drift?
Structural analysis
Molecular Dynamics Simulation
From static poses to dynamic behaviour.
Simulation of stability and interaction persistence over time. A docked pose is a single frame; a trajectory shows whether it holds together.
Why molecular dynamics?
A static structure can't tell a persistent interaction from one that merely looks right in a single frame.
Questions we answer
Analytical questions about the simulated system, not guaranteed outcomes.
Do interactions persist?
Which contacts survive a meaningful fraction of the run.
Which residues matter?
Per-residue involvement across the trajectory.
Does the complex rearrange?
Whether it settles into a different binding mode.
How do candidates compare?
Relative behaviour under matched conditions.
Our MD services
The molecular systems we simulate. Drag a model to turn it.
Protein–Ligand
How a bound ligand and its pocket contacts behave through the run.
Enquire about Protein–Ligand simulationsProtein–Protein
Interface contacts and how consistently they hold.
Enquire about Protein–Protein simulationsAntibody–Antigen
CDR loop flexibility and paratope–epitope contacts.
Enquire about Antibody–Antigen simulationsMutation / Variant
Matched wild-type and variant runs, compared side by side.
Enquire about Mutation / Variant simulationsFree-Energy
Sampling of energetic states, reported comparatively.
Enquire about Free-Energy simulations
Illustrative MD simulations of each system type, not outputs from an actual run.
6 stages
End-to-end MD package
- 01
System Preparation
The structure is protonated, solvated, and parameterised with a suitable force field.
- 02
Equilibration
Minimisation, heating, and density equilibration bring the system to stable conditions.
- 03
Production Simulation
A GPU-accelerated run at the agreed length and replicate count.
- 04
Trajectory Analysis
Deviation, flexibility, contacts, and collective motion are quantified.
- 05
Energetic Analysis
End-state free-energy estimates, where appropriate, for comparison.
- 06
Reporting
Protocol, results, figures, and limitations in one report.
What we analyse
- Backbone Cα · mean ± SD across replicas (shaded)Illustrative visualization
Measures overall structural deviation relative to a reference structure across the trajectory. It depends on the reference and the atoms selected, and a low value alone does not show a structure is stable.
Applications of molecular dynamics
Docking Pose Assessment
Check whether a docked pose is maintained and its contacts persist during the simulation. This is consistent with, not proof of, binding.
Antibody–Antigen Dynamics
Characterise Fv–antigen interfaces, CDR contacts, and binding behaviour through the run.
Protein–Protein Interaction Analysis
Follow interface stability, residue contacts, and hydrogen-bond networks across the trajectory.
Candidate Prioritization
Compare candidates on RMSD, contact persistence and energetic estimates as inputs to experimental selection, not as a ranking of activity.
Mutation & Variant Analysis
Evaluate how sequence changes affect stability, flexibility, and binding interfaces.
Binding & Free-Energy Analysis
Approximate binding-energy contributions with MM-PBSA/MM-GBSA and residue-level decomposition. These are end-point approximations, not absolute affinities.
Protein Stability & Conformational Dynamics
Capture flexibility and conformational states that a single static structure can't show.
Mechanistic & Structural Studies
Uncover dynamic interaction networks and conformational transitions behind molecular recognition.
Lead Optimization
Compare binding modes and dynamic behaviour across a candidate series to guide design.
Biologics & Protein Engineering
Assess engineered antibodies and proteins for interface behaviour and stability.
Animated visuals are illustrative MD simulations, not outputs from an actual run.
Conformational dynamics
Protein Stability & Conformational Dynamics
A crystal or docked structure is one snapshot. Over a trajectory the same protein flexes, rearranges and moves between conformational states, which MD resolves and quantifies.
Deliverables
- Trajectory
- Analysis results
- Scientific visualisations
- Interaction analysis
- Energetic analysis, where applicable
- Final report
Have a target in mind?
Custom MD simulations that report flexibility, interaction persistence and conformational behaviour over the simulated time.