The open-source framework for fragment-based generation of chemical structures. The idea is similar to matched molecular pair - if two fragments are in the identical contexts they can replace each other to produce new chemically valid and probably synthetically feasible structures.
Features:
Implementation features:
These databases were created using CReM 0.2 and RDKit 2019.09.3 but they should be compatible with RDKit 2018.09 as well. They are not compartible with RDKit 2017.09 (due to different SMILES canonicalization). All databases contain data for contexts of radius 1, 2 and 3.
task | SMILES LSTM* | SMILES GA* | Graph GA* | Graph MCTS* | CReM |
---|---|---|---|---|---|
Celecoxib rediscovery | 1.000 | 0.732 | 1.000 | 0.355 | 1.000 |
Troglitazone rediscovery | 1.000 | 0.515 | 1.000 | 0.311 | 1.000 |
Thiothixene rediscovery | 1.000 | 0.598 | 1.000 | 0.311 | 1.000 |
Aripiprazole similarity | 1.000 | 0.834 | 1.000 | 0.380 | 1.000 |
Albuterol similarity | 1.000 | 0.907 | 1.000 | 0.749 | 1.000 |
Mestranol similarity | 1.000 | 0.79 | 1.000 | 0.402 | 1.000 |
C11H24 | 0.993 | 0.829 | 0.971 | 0.410 | 0.966 |
C9H10N2O2PF2Cl | 0.879 | 0.889 | 0.982 | 0.631 | 0.940 |
Median molecules 1 | 0.438 | 0.334 | 0.406 | 0.225 | 0.371 |
Median molecules 2 | 0.422 | 0.38 | 0.432 | 0.170 | 0.434 |
Osimertinib MPO | 0.907 | 0.886 | 0.953 | 0.784 | 0.995 |
Fexofenadine MPO | 0.959 | 0.931 | 0.998 | 0.695 | 1.000 |
Ranolazine MPO | 0.855 | 0.881 | 0.92 | 0.616 | 0.969 |
Perindopril MPO | 0.808 | 0.661 | 0.792 | 0.385 | 0.815 |
Amlodipine MPO | 0.894 | 0.722 | 0.894 | 0.533 | 0.902 |
Sitagliptin MPO | 0.545 | 0.689 | 0.891 | 0.458 | 0.763 |
Zaleplon MPO | 0.669 | 0.413 | 0.754 | 0.488 | 0.770 |
Valsartan SMARTS | 0.978 | 0.552 | 0.990 | 0.04 | 0.994 |
Deco Hop | 0.996 | 0.970 | 1.000 | 0.590 | 1.000 |
Scaffold Hop | 0.998 | 0.885 | 1.000 | 0.478 | 1.000 |
total score | 17.341 | 14.398 | 17.983 | 9.011 | 17.919 |
Polishchuk, P., CReM: chemically reasonable mutations framework for structure generation. Journal of Cheminformatics 2020, 12, (1), 28. - https://doi.org/10.1186/s13321-020-00431-w