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3D ligand-based molecular design

Understand binding conformations to identify and optimise novel active compounds

StarDrop’s eSim3D module

eSim3D™ supports your 3D ligand-based design efforts, providing intuitive workflows to:

Enable 3D design, even with little or no target structure information
Find novel active compounds with 3D virtual screening against known actives
Understand 3D SAR with industry-leading pose prediction
Generate binding mode hypotheses by alignment of multiple known actives
Complement structure-based compound design approaches with a ligand-centred perspective

State-of-the-art molecular similarity

Based on surface-shape, electrostatics and directionally-sensitive hydrogen-bonding, the eSim method enables accurate surface-based comparison of molecules. This scaffold-independent method mimics a protein’s perspective of a ligand, improving the accuracy of pose prediction, virtual screening and multiple ligand alignment compared to other molecular similarity methods.

High-performance 3D virtual screening

Screen millions of compounds, direct from your desktop, in a matter of minutes. eSim’s virtual screening methods have been proven to achieve high enrichment compared to other market platforms. With 3D conformers pre-generated from our vendor library using ForceGen technology, you can screen large collections of purchasable compounds to quickly identify scaffold hops and novel actives.

Visit the virtual screening downloads section of our site to access prepared virtual screening collections for use in StarDrop.

Virtual screening collections

Accurate pose prediction

Quickly identify the correct molecular alignments. Embedded with physically-meaningful underlying factors, eSim’s pose prediction capabilities have been shown to significantly outperform alternative methods, as proven in several published peer-reviewed benchmarking and validation studies.

Multiple ligand alignment

Align multiple known active ligands to generate binding pose hypotheses. These ensembles can be used as targets for virtual screening and to improve our understanding of 3D structure-activity relationships to guide lead selection and optimisation.

Structure- and ligand-based virtual screening on DUD-E+: performance dependence on approximations to the binding pocket

Using the DUD-E+ benchmark, we explore the impact of using a single protein pocket or ligand for virtual screening compared with using ensembles of alternative pockets, ligands, and sets thereof.

Challenges and approaches in 3D ligand-based drug design

Ann and Ajay discuss the science behind and applications of the eSim molecular similarity method, a ligand-based drug design approach which considers surface-shape, electrostatics, and directionally sensitive hydrogen-bonding when comparing two molecules.

MolPort screening collection

StarDrop users who have licensed the Surflex eSim3D module can freely download prepared virtual screening collections for use in StarDrop. MolPort’s commercially available screening…

Interested in 3D ligand-based design?

Would you like to try the eSim3D module? Complete the form and a member of the team will get in touch to discuss your needs.

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