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LBDD: Ligand-Based Drug Design

What is Ligand-Based Drug Design (LBDD)

Ligand-Based Drug Design (LBDD) is a computational approach that leverages knowledge of existing ligands, or small molecules that bind to biological targets, to design and optimize new drug candidates. By comparing known ligands, researchers can predict how similar molecules will interact with the same target, offering faster insights and improving lead discovery.
Essentially, Similar Ligands = Chance to target the same structure

No Target Structure? No Problem!

Our product portfolio features several powerful applications facilitating LBDD in the 2D and 3D world.

2D – Mining Chemical Spaces for similar compounds


We have developed several methods to retrieve similar compounds to a query structure from trillion-sized molecule collections based on the needs of the project.

3D – Molecule superpositioning


Align a set of molecules to a conformation of your template ligand to match its shape and features.

Dive into the Largest Hunting Grounds for Drug-Like Compounds: Chemical Spaces

Chemical Spaces are combinatorial compound clusters featuring trillions of entries.

We at BioSolveIT develop methods to screen these vast molecule collections for relevant chemistry. Our Chemical Space navigation platform infiniSee retrieves similar and accessible compounds tailored to the aims of the projects.

  • infiniSee: Our core Chemical Space navigation platform, infiniSee, enables fast and efficient exploration of vast combinatorial molecular spaces, finding relevant and accessible compounds tailored to your research goals.
  • Scaffold Hopper: Discover new chemical scaffolds that maintain the core features of your query molecule while offering novel structures for drug discovery.
  • Analog Hunter: Locate and evaluate similar compounds (analogs) based on the chemical and biological activity of your input molecule, streamlining the lead optimization process.
  • Motif Matcher: Identify and retrieve compounds containing specific molecular motifs or substructures, enabling focused exploration of chemical spaces based on functional groups.

    • All search modes are also available as command-line versions for integration into automated workflows and high-throughput screening pipelines.

Explore Shape Similarities and Functional Overlaps with SeeSAR

Another way to assess the similarity between two molecules is by using 3D methods to align them and score how well they overlap.

In our drug discovery dashboard SeeSAR and its Similarity Scanner Mode, users can perform ligand-based virtual screening to find the most similar compounds based on features like shape, aromaticity, and arrangement of H-bond donors and acceptors. With FlexS, one of SeeSAR's core components, users can further improve this process by docking ligands flexibly into a protein binding site, optimizing how well they align and interact with their targets.

Fill Your Drug Discovery Pipeline with BioSolveIT!

Ready to take your ligand-based projects to the next level?

Experience the power of BioSolveIT’s applications and accelerate your drug discovery process.

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