MOLECULAR DYNAMICS
Simulations

Physical modelling of molecular motion, interactions and binding-site behavior.

Explore how molecular systems move, interact and respond over time.

Molecular dynamics simulations add a time dimension to structural biology. Instead of looking only at a static structure, they show how proteins, complexes, ligands or binding sites behave under defined conditions.

At BIMOVIS, we use molecular simulations to investigate questions where motion, flexibility or interaction dynamics matter. This can include key residue interactions, binding mechanisms, on- and off-target interactions, binding-site flexibility or the structural basis of molecular recognition.

Our simulations are developed in close connection with experimental and computational structural biology. Where available, we integrate information from cryo-EM, X-ray crystallography, AI structure prediction, biochemical data or existing structural models to make the simulation setup biologically meaningful and relevant to the project question.

Depending on the system, simulations can be adapted across different levels of detail, from highly resolved binding-site analysis to larger molecular assemblies where broader structural behavior is the focus.

Dynamics, flexibility and interaction mechanisms beyond a static structure.

Molecular dynamics simulations help explore how molecular systems behave after a structure has been determined or predicted. They can reveal whether a binding pocket remains open, how a ligand stabilizes a conformation, which residues contribute to an interaction or how structural changes propagate through a protein.

For drug discovery, protein engineering and model interpretation, this adds context that is difficult to obtain from a single structure alone. A model may show where atoms are placed, but molecular simulation helps assess how stable, flexible or functionally relevant that arrangement is.

At BIMOVIS, we interpret simulation results in the context of the scientific question, not as isolated computational output. The aim is to generate insight that supports decisions around binding, specificity, stability, mechanism or further experimental work.

Protein flexibility, conformational changes and structural dynamics
Binding-site behavior and pocket accessibility
Key residue interactions and interaction networks
Ligand binding mechanisms and stability of binding poses
On-target and off-target interaction hypotheses
Structural context for experimental data, AI-generated models and design decisions

How we work.

Question & input review

We define the scientific question and review available structures, models, experimental data and project context.

System preparation

We assess the binding site, prepare the structural model and define whether structure-based, ligand-based or combined screening is most appropriate.

Simulation strategy

We select the simulation approach, level of detail and timescale based on the molecule, question and required readout.

Molecular dynamics simulation

The system is simulated under defined conditions to explore molecular motion, stability and interaction behavior over time.

Analysis of dynamics and interactions

We review predicted poses, interaction patterns, chemical diversity and practical follow-up criteria to select the most relevant candidates.

Interpretation & next steps

Results are interpreted together with structural, biochemical or computational information to support the next scientific decision.

Question & input review

We define the scientific question and review available structures, models, experimental data and project context.

System preparation

The molecular system is prepared for simulation, including structure curation, protonation states, ligand setup, membrane or solvent environment where relevant.

Simulation strategy

We select the simulation approach, level of detail and timescale based on the molecule, question and required readout.

Molecular dynamics simulation

The system is simulated under defined conditions to explore molecular motion, stability and interaction behavior over time.

Analysis of dynamics and interactions

We analyze conformational changes, residue interactions, binding-site flexibility, ligand behavior or other project-relevant features.

Interpretation & next steps

Results are interpreted together with structural, biochemical or computational information to support the next scientific decision.

Where this service applies.

Molecular dynamics simulations support projects where motion, flexibility or interaction behavior are central to the structural biology question.

Structure-Based Drug Design

Simulation-based insight into binding-site flexibility, ligand stability and interaction mechanisms for structure-guided discovery.

Protein Engineering

Assessment of structural stability, conformational behavior and interaction changes in engineered proteins or variants.

PROTAC Design

Dynamic analysis of binding events, linker behavior or structural hypotheses relevant to degrader design.

AI Structure Model Validation

Evaluation of predicted structures by exploring stability, flexibility and consistency with available structural or experimental information.

Antibody Epitope Mapping

Support for understanding interaction dynamics, interface behavior and structural hypotheses around antibody-antigen recognition.

Molecular dynamics questions.

When is molecular dynamics simulation useful compared with a static structure?

Molecular dynamics simulation is useful when the main question involves motion, flexibility, stability, or interaction behavior over time. A static structure can show where atoms sit, but MD can help explore whether a binding pocket stays open, whether a ligand pose remains stable, how residues interact over time, or how shape changes may affect function.

What types of input data can be used to set up an MD simulation project?

MD simulation projects can use experimental structures, AI models, existing structural models, and relevant biochemical or project data. Information from cryo-EM, X-ray data, AI structure prediction, and experimental results can help make the setup biologically meaningful and aligned with the scientific question.

What kinds of questions can BIMOVIS investigate with molecular dynamics simulations?

BIMOVIS can investigate protein flexibility, shape changes, binding-site access, ligand binding stability, key residue interactions, interaction networks, on-target and off-target ideas, and the structural basis of molecular recognition. The analysis is built around the project goal rather than treated as stand-alone output.

How can molecular dynamics support drug discovery or protein engineering?

In drug discovery, MD can give insight into binding-site flexibility, ligand stability, binding mechanisms, and interaction behavior that may shape design. In protein engineering, it can help assess how variants or engineered proteins affect structural stability, shape behavior, and molecular interactions.

How are MD simulation results interpreted?

Results are interpreted in the context of the original scientific question and combined with available structural, biochemical, experimental, or in-silico information. The goal is to support decisions about binding, specificity, stability, mechanism, model reliability, or the next experimental or model steps.

Can molecular dynamics simulations be performed on AI-predicted protein structures?

Yes, when the predicted structure is sufficiently suitable for the scientific question. BIMOVIS can assess an AI-generated model before simulation, identify regions of uncertainty, and use appropriate simulation and analysis strategies to explore stability, flexibility, binding-site behavior, or other project-relevant dynamics.

Extend your project.

AI Structure Prediction & Model Analysis

Predicted structures and model assessment as starting points or reference models for simulation-based analysis.

Structure Analysis & Model Validation

Expert evaluation of experimental structures, AI-generated models and simulation outputs in the context of the scientific question.

Virtual Screening

Computational screening approaches that can be complemented by molecular dynamics to assess binding poses and interaction behavior.

Go deeper in our Knowledge Hub.

Guides, protocols, and reference materials to support your structural biology projects — free to access.

MOLECULAR DYNAMICS Simulations