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Overview
This dataset contains Functional Group (FG)-enhanced SMILES designed for molecule representation learning. It consists of approximately 200 million FG-enhanced SMILES collected from a wide range of chemical suppliers and databases, as detailed below:
Supplier | Number of Compounds | Source |
---|---|---|
Targetmol | 22,555 | Targetmol |
Chemdiv | 1,741,620 | Chemdiv |
Enamine | 862,698 | Enamine |
Life Chemical | 347,657 | Life Chemicals |
Chembridge | 1,405,499 | Chembridge |
Vitas-M | 1,430,135 | Vitas-M |
InterBioScreen | 560,564 | InterBioScreen |
Maybridge | 97,367 | Maybridge |
Asinex | 601,936 | Asinex |
Eximed | 61,281 | Eximed |
Princeton BioMolecular | 1,647,078 | Princeton BioMolecular |
Otava | 9,203,151 | Otava |
Alinda Chemical | 733,152 | Alinda Chemical |
ChEMBL 25 | 1,785,415 | ChEMBL |
ZINC15 | 175,000,000 | ZINC15 |
Total | 200,000,000 |
Dataset Details
This dataset contains 42,364 unique tokens (vocabulary size = 42,364), which is an extension from 93 tokens in the corresponding standard SMILES dataset. This expansion helps bridge the gap between SMILES and natural language, which has a large set of vocabulary to sufficiently express the nuances of language.
Examples of FG-enhanced SMILES
Below are some examples of FG-enhanced SMILES from the dataset. Each SMILES string is augmented with functional group annotations (e.g., C_alkyl
, O_ether
, c_6
, n_tertiary_amine
, etc.) to enhance the representation of molecular structures for machine learning models.
C_alkyl O_ether c_6 1 c_6 c_6 c_6 ( - c_5-6 2 n_5-6 c_5-6 3 n_tertiary_amine_5-6 ( C_alkyl c_6 4 c_6 c_6 c_6 c_6 c_6 4 F_fluoro ) c_5-6 ( C_alkyl ) c_5-6 ( - c_5-6 4 c_5-6 c_5-6 c_5-6 5 c_5-6 ( c_5-6 4 ) O_ether_5-6 C_5-6 O_ether_5-6 5 ) c_amide_5-6 ( = O_amide ) n_amide_5-6 3 c_5-6 2 C_alkyl N_tertiary_amine ( C_alkyl ) C_alkyl C_alkyl c_6 2 c_6 c_6 c_6 c_6 c_6 2 ) c_6 c_6 1
C_alkyl C_tertiary_carbon ( C_alkyl ) C_tertiary_carbon ( C_ester ( = O_ester ) O_ester C_ester c_5-6 1 c_5-6 n_tertiary_amine_5-6 2 c_5-6 c_5-6 c_5-6 c_5-6 c_5-6 2 n_5-6 1 ) C_tertiary_carbon ( C_alkyl ) N_secondary_amine C_ester ( = O_ester ) O_ester C_ester ( C_alkyl ) ( C_alkyl ) C_alkyl
C_alkyl C_tertiary_carbon_6 1 C_6 N_tertiary_amine_6 ( c_5 2 n_5 n_5 c_5 ( C_tertiary_carbon_3 3 C_3 C_3 3 ) n_tertiary_amine_5 2 C_alkyl C_alkyl N_secondary_amine C_ketone ( = O_ketone ) c_5 2 c_5 c_5 c_5 s_5 2 ) C_6 C_amide_6 ( = O_amide ) N_amide_6 1 C_alkyl
C_alkyl O_ether C_alkyl C_alkyl n_tertiary_amine_5 1 c_5 ( C_alkyl c_5 2 c_5 c_5 ( C_alkyl ) n_secondary_amine_5 n_5 2 ) n_5 n_5 c_5 1 N_tertiary_amine_7 1 C_7 C_7 C_7 N_amide_7 ( C_amide ( = O_amide ) C_tertiary_carbon ( C_alkyl ) C_alkyl ) C_7 C_7 1
C_alkyl C_alkyl n_amide_6-6 1 c_amide_6-6 ( = O_amide ) n_6-6 c_6-6 ( O_hydroxyl ) c_6-6 2 c_6-6 ( C_ketone ( = O_ketone ) N_secondary_amine N_tertiary_amine_5 3 C_5 C_5 C_5 C_tertiary_carbon_5 3 C_alkyl O_ether C_alkyl ) c_6-6 c_6-6 ( C_tertiary_carbon ( C_alkyl ) C_alkyl ) n_6-6 c_6-6 1 2
C_alkyl C_tertiary_carbon_3 1 C_3 C_tertiary_carbon_3 1 C_alkyl n_tertiary_amine_5 1 c_5 ( C_alkyl c_6 2 c_6 c_6 n_6 c_6 c_6 2 ) n_5 n_5 c_5 1 N_tertiary_amine_6 1 C_6 C_6 N_tertiary_amine_6 ( C_alkyl C_amide ( = O_amide ) N_amide ( C_alkyl ) C_alkyl ) C_6 C_6 1
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