SkelGen – A Newly Available Tool for Computational Drug Design

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drug designWith the rapidly growing body of biostructural information, structure-based drug design has increased in importance and a variety of computational methods have found a place in the drug discovery toolkit.

The de novo design program, SkelGen, was developed by De Novo Pharmaceuticals based on research begun in the Department of Pharmacology at the University of Cambridge. SkelGen constructs candidate ligands by assembling small molecular fragments within a protein target such as an enzyme or receptor (usually derived from X-ray crystal data). When growing a ligand, SkelGen uses information coded in the fragments and within its algorithm to favour synthetically tractable molecules. SkelGen is able to explore around one trillion low molecular weight, drug-like molecules using a default set of 1600 fragments. Since the accessible chemical space is so large, the majority of designed molecules are novel and patentable.

Whilst SkelGen can be run with minimal input, it also permits extensive control by the end-user, allowing the scientist to incorporate prior knowledge and insights into the drug design process. As well as completely de novo design, molecule generation can also be started from a user-defined fragment (for example, a low-affinity molecule identified by fragment-screening). SkelGen can also be used for scaffold hopping (chemotype switching) and focused library design.

Until recently SkelGen was only accessible through collaborations with De Novo Pharmaceuticals but is now available under both academic and commercial licenses. With these new licensing models, SkelGen can be a cost-effective (and accessible) tool for all scientists engaged in drug design. If you would like to find out more about SkelGen, please contact us.


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