On the Art of Compiling and Using 'Drug‐Like' Chemical Fragment Spaces

By J. Degen, C. Wegscheid‐Gerlach, A. Zaliani, Matthias Rarey. ChemMedChem, 2008

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Computational Methods in Drug Discovery (2014, methodology): “…Procedure) was the first fragment generation method to incorporate rules that limit the chemical reactions to ones used in typical combinatorial chemistry techniques, thereby limiting the possible fragments as well as possible recombination patterns (Lewell et al., 1998; Degen et al., 2008).”
Shape-Based Generative Modeling for de Novo Drug Design (2019, neutral): “Fragment 49 and sca ﬀ old 50 frequencies as well as similarity to the nearest neighbor are also close to those for other methods.”
Structure-based drug design with equivariant diffusion models (2022, positive): “The molecule is broken into three fragments using the Breaking Retrosynthetically Interesting Chemical Substructures (BRICS) (Degen et al., 2008) protocol.”
GuacaMol: Benchmarking Models for De Novo Molecular Design (2018, background): “13,26,27 This, however, may drastically limit the potentially ex-plorable space.”
Equivariant 3D-conditional diffusion model for molecular linker design (2022, positive): “The MMPA-based algorithm 40 and BRICS 41 used for molecule fragmentation, as well as force field relaxation procedure MMFF 46 52 .”