Evaluating properties of molecular fingerprints using Neural Mutual Information estimation.
Traditional Fingerprints
| Name | Length | Type | Software |
|---|---|---|---|
| AP2DC | 780 | PaDEL | |
| E-state | 79 | RDKit | |
| KRC | 4860 | PaDEL | |
| MACCS | 166 | PaDEL | |
| PubChem | 881 | PaDEL | |
| SSC | 307 | PaDEL |
Machine Learning representations
| Name | Length | Code |
|---|---|---|
| MolBERT (v1, v2) | - | Available |
| MolXPT | - | ??? |
| GIN (Graph Contrastive) | - | Implement |
| Dataset | Length | N Properties | Properties |
|---|---|---|---|
| ESOL | 1128 | 1 | Solubility in water |
| FreeSolv | 642 | 1 | Hydration free energy |
| Lipophilicity | 4200 | 1 | ocatnol/water distribution coefficient |
| PCBA | 437929 | 128 | Measured biological activities of small molecules |
| BACE | 1513 | 1 | binding results for beta-secretase |
| BBBP | 2039 | 1 | Blood-brain barrier penetration |
| Tox21 | 7831 | 12 | toxicity measurements on 12 biological targets |
| ToxCast | 8575 | 617 | toxicology data for different tasks |
| SIDER | 1427 | 27 | Marketed drugs and adverse drug reaction |
| ClinTox | 1478 | 2 | Qualitative data of drugs approved and failed by FDA |
| FishTox | - | - | Fish toxicity measurements |
Selection:
- FishTox
- SIDER
- BBBP
- ESOL
- Lipophilicity
- PCBA
conda env createconda activate InfoMolexport PYTHONPATH=.python scripts/compute_mi.py --help
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