README.md

metadata

license: mit
dataset:
  - chembl
  - zinc15

Overview

This dataset contains Functional Group (FG)-enhanced SMILES designed for molecule representation learning. It consists of approximately 20 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	4,000,000	ZINC15
Total	20,000,000

Dataset Details

This dataset contains 36,748 unique tokens (vocabulary size = 36,748), 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.

For more details about the method of generating FG-enhanced SMILES, please refer to our paper, FARM: Functional Group-Aware Representations for Small Molecules, or visit our GitHub repository for implementation details.

Below is a breakdown of the number of token types that represent different chemical elements: Number of functional groups associated with different chemical elements in the FG-enhanced SMILES dataset. The y-axis represents the natural logarithm (log, base e) of the count.

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.

1. 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

2. 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

3. 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

4. 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

5. 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

6. 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