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EAI-TupletScore, a pharmacophore and shape driven ligand-based de-novo design algorithm

We describe a ligand-based de-novo design algorithm EAI-TupletScore and studies that demonstrate its ability to successfully generate lead hops between different classes of active ligands from the DUD dataset [1]. EAI-TupletScore uses the de-novo design engine EA-Inventor with a Pareto-Borda [2][3] scoring method that employs pharmacophore and steric tuplets [4], as well as UNITY fingerprint similarities to a set of lead compounds to design novel ligands that maximize pharmacophore and shape similarity, while maintaining a certain level of structural dissimilarity, to these lead compounds. EAI-TupletScore, can be used to design novel ligand scaffolds (lead generation or lead hopping) or to optimize attachments on a fixed scaffold (lead optimization).


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Open Access This article is distributed under the terms of the Creative Commons Attribution 2.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Smith, K., Masek, B., Clark, R. et al. EAI-TupletScore, a pharmacophore and shape driven ligand-based de-novo design algorithm. Chemistry Central Journal 3 (Suppl 1), P29 (2009).

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