Another easy thing for medicinal chemists to talk about is the ‘scaffold’ of the molecule, or indeed ‘scaffold hopping’. Between chemists it might be possible to build a fair definition, which works well until the next weird ‘chemical class’ appears for a new set of protein targets. For chem-informaticians working in computer space the encoding of a scaffold needs to be firmly defined to script programs that work consistently across chemical space. The technical approach to breaking down organic molecules to defined scaffolds described in this paper is so well done that we talk about ‘Bemis / Murcko scaffolds’. So if you want to know how it is done and use the scaffolds then you had better read this paper.
Bemis, G.W.; Murcko, M.A.; The Properties of Known Drugs. 1. Molecular Frameworks J. Med. Chem.1996, 39, 15, 2887-2893
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