STRUCTURE-BASED
Drug Design

Molecular insight for hit discovery, hit-to-lead and lead optimization.

Binding modes

Chemical starting points

Pocket behaviour

Model confidence

From structure to design decisions.

Structure-based drug design uses three-dimensional information to guide compound design, prioritization and optimization. When a target-ligand interaction is understood at molecular level, medicinal chemistry decisions become more focused: which interactions should be preserved, where chemical changes are possible and how selectivity or potency may be improved.

Structural insight supports many stages of early discovery. It can validate hits from screening campaigns, reveal fragment binding modes, identify ligandable pockets or explain why compounds behave differently in assays. It also helps connect activity data with molecular interpretation, which is often the point where structure-based drug design becomes most useful.

At BIMOVIS, we approach SBDD through the question behind the program. Some projects need high-resolution protein-ligand structures. Others benefit from virtual screening, crystallographic fragment screening, AI-supported model analysis, molecular dynamics simulations or validation of existing structural data. The strongest value often comes from combining these approaches in a way that fits the target, the available information and the current design decision.

Our goal is not only to generate structures. It is to make structural information useful for the next medicinal chemistry step.

Where structural biology supports SBDD.

HIT VALIDATION

Hit validation

A compound hit becomes more informative when its binding mode is understood. Structural biology helps confirm where and how a molecule binds, whether the interaction is plausible and which residues or subpockets matter for follow-up.

Fragment-to-hit

Crystallographic fragment screening and binding-site analysis can reveal early chemical starting points. Even weak binders become valuable when their position, orientation and interaction pattern are structurally defined.

HIT-TO-LEAD

Hit-to-lead and lead optimization

Protein-ligand structures help connect SAR with molecular detail. They show how chemical changes affect the binding site and provide a rational basis for improving potency, selectivity or physicochemical properties.

POCKET ANALYSIS

Binding-site and pocket analysis

Structural data can identify ligandable pockets, alternative binding sites and flexible regions that may not be obvious from sequence or assay data alone. This is especially useful for difficult, dynamic or less explored targets.

MODEL-INFORMED DESIGN

Model-informed design

AI-generated models and computational structures can support early hypotheses, but they need careful interpretation before being used for docking, virtual screening or design. Model validation helps define what can be used with confidence and where experimental evidence is needed.

Let’s work together

Start with your structural question.

Bring us your target, compound series, fragment hits, predicted model or design challenge. We help identify which structural biology approach is most useful for the next medicinal chemistry decision.

Extend your project.

X-ray Crystallography

Resolve protein-ligand structures at atomic detail to support binding-mode analysis and lead optimization.

Crystallographic Fragment Screening

Identify experimentally observed fragment binding modes as early chemical starting points.

Virtual Screening

Prioritize compounds and generate testable binding hypotheses for experimental follow-up.

Go deeper in our Knowledge Hub.

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

STRUCTURE-BASED Drug Design