Dataset Viewer
Auto-converted to Parquet
id
large_stringlengths
1
16
SMILES
large_stringlengths
1
814
178049108
OC1=NNC(c2ccc(-c3ccncc3)c(C(F)(F)F)c2)=NC1
146248503
Cl.NC1CCC(C(=O)Nc2ccc(S(=O)(=O)NCC3CC3)cc2)C1
157646512
C[C@H](N=C(O)[C@H]1CCCC(O)=N1)c1ccc2c(c1)OCCO2
123389910
CC(NC(=O)c1ccc(-c2ccccc2)nc1O)c1ccc2c(c1)CC(O)=N2
68308015
COc1ccc(/C=N\n2c(S)nnc2Cc2ccc(F)cc2)cc1OC
113125914
C#CC(CCC)N=C(O)Nc1ccc(C(=O)O)cc1C
113522590
CCN(CC1CCCNC1)C(=O)/C=C/c1ccc(Cl)cc1
24501851
COc1cc(/C=C2\C(=N)N3N=C(S(C)(=O)=O)SC3=NC2=O)ccc1OCc1ccc(Br)cc1
149383128
COC(=O)c1ccc(NC2=C(Cl)C(=O)N(c3ccc(OC)c(OC)c3)C2=O)cc1
157927709
CCN[C@@]1(CN)CC[C@H]2C[C@H]1C2(C)C
110899002
CCCNC=C1C=C(OCCOCCOCCOC)C(CC2=NC(=CNCCC)C=C2OCCOCCOCCOC)=N1
MCULE-1501827169
CCOc1ccc(-c2cnn3c(N)c(C#N)c(SC)nc23)cc1
43880743
C=CC[C@H](Cc1ccccc1)C(=O)O[C@H]1[C@@H](OC(=O)[C@H](CC=C)Cc2ccccc2)[C@@H](CO)O[C@H](OC)[C@@H]1OC(O)=Nc1ccccc1
149399265
Cc1cc(C)c(C#N)c(SC2=C(Nc3ccc(F)cc3F)C(=O)N(c3cccc(C#N)c3)C2=O)n1
128286547
CCOCCCC(O)=NC(C)CSC
92326367
OCC1CCCCN1c1ncnc(O)c1Br
MCULE-9776234064
Oc1cccc(-c2ccsc2C(F)F)c1F
5375074
Cc1[nH]c2ccc(CN=C(O)N3CCN(c4cc(C#N)ccn4)CC3)cc2c1C
21692800
Cc1cnn(C2CN(C[C@@](C)(O)c3ccccc3)C2)c1
80332500
FC(F)(F)Sc1cc(I)ncc1C(F)(F)F
79971223
C#CC1=c2cc3c(cc2-c2ccccc21)=C(C#C)c1ccccc1-3
112097063
OC(=NCCN1CCSCC1)c1ccc(F)cc1O
110430237
C[C@H](CN=C(O)COc1ccccc1C#N)c1nc2ccccc2s1
48665056
CS(=O)(=O)c1cccc(C(Br)c2cc(F)c(Br)cc2F)c1
176495657
CC.Cc1ccc(OC(C)CCC(C)C(C)CCC(C)C)c(C)c1
MCULE-8466319730
COc1cc(CC(O)=Nc2ccccc2N2CCN(C)CC2)c(-c2ccncc2F)cc1OC
48385032
CCCCCCC(C)O[Si](C)=C1C=C[C](CC)C=C1
76853363
O=C(CSc1ccc(N=C(O)C(=Cc2ccsc2)N=C(O)c2ccccc2)cc1)N(c1ccccc1)c1ccccc1
183374643
CCC1OC1OCOC1OC1CC
174218513
O=C(O[C@H]1CN[C@H](C#Cc2cc3ncnc(Nc4ccc(OCc5cccc(F)c5)c(Cl)c4)c3s2)C1)N1CCS(=O)(=O)CC1
76310675
CC1(C)OC2C(O1)C(CO)(CO)OC2[N+]1(C2OC(CO)C(O)C2O)C=CC(O)=NC1=O
169758129
CC(C)(C)N1C(c2ccccc2)N(C(C)(C)C)[SiH]1Cl
189836175
[3H]OC(C)=NC1C(C=C)=C(/C=C/C)Oc2cc(N=[N+]=[N-])ccc21
9406046
CCC(O)=Nc1cccc(NC(=O)C(=O)N[C@@H](C)Cc2ccc(O)cc2)c1
718929
N=C(N)N/N=C(/C=C/c1ccc(OCc2ccccc2)cc1)c1ccccc1
27643348
CC(=O)OCC[C@H](CC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CCC4CCCC[C@]4(C)[C@H]3CC[C@]12C)C(C)C
151628397
COc1ccc([C@@H]2Cn3nnc(C(=O)N4CCN(c5ccccc5F)CC4)c3CO2)cc1
87400342
COc1cncc(C(=O)Cc2ccc(Br)cc2)c1
87059363
N=C(NO)c1cc(OC2CCCC2)ccc1C(F)(F)F
110246430
Cc1noc2nc(-c3ccccc3F)cc(C(O)=NCCCc3cnn(C)c3)c12
80394082
Cc1ccccc1C(=O)Nc1ccc(C(=O)OC2CCNCC2)cc1.Cl
52883966
CC(C)CC(N=C(O)C1COCC1N)C(=O)O
192630741
CCC(C)(C(=O)[O-])S(C)(=O)=O.O.[K+]
42373443
N=C(O)CN1CCC(N=C(O)c2cc(Cl)ccc2F)CC1
13312193
CS[C@H](C)c1cccc(N=C(O)CNc2ccccc2[N+](=O)[O-])c1
122187833
COCCN=C(O)CN=C(O)c1ccc(C)c(Cl)c1
151767821
COc1ccc(C2=NN=C(C(=O)N/N=C\c3ccccc3Br)C2)cc1
135768623
Cc1c(N=C(O)C=Cc2ccc3c(c2)OCCO3)cccc1N(C)C
96235201
CSCC(C)N(C)C(=O)N1CCCCC1C(=O)O
28279198
COC(=O)Oc1c[nH]c2c(O)nc3ccc(S(=O)(=O)NC4CCNCC4)cc3c12
125969691
Cc1ccccc1-c1nc(CNc2cc(Cl)ccc2OCC2CCOC2)no1
61165929
CC(C)N(C(=O)CSC1=N[C@H](c2ccccc2)C2=C(N1)/C(=C/c1ccccc1)CCC2)c1ccccc1
609154
COc1cc(N)c(Cl)cc1C(O)=NCC1CN(Cc2ccc(C(F)(F)F)cc2)CCO1
118177179
C=CCN(CCO)C(O)=Nc1cccc(C(C)C)c1
81926933
COc1cncnc1-c1cnn(C)c1C(=O)Nc1cc2nc(-c3ccccc3)nn2cc1F
MCULE-6089265252
CSc1ncc(-c2cccc3c2cnn3C)c(C(=O)N2CCN(c3ccc(C#N)cc3)CC2)n1
MCULE-3420227037
OC(=NCCCCN1CCCC1)c1cccc(N=C(O)c2ccccc2)c1
99732855
[B+]=C1C=CC(=N[O-])C=C1CN(C)C(=O)C(Nc1ccc2ccnc(O)c2c1)c1ccc([C@@H](C)CCC)c(C)c1
142421599
COC(=O)c1ccc(F)cc1S(=O)(=O)NCCCc1ccccc1
MCULE-7076717356
Cc1cc(F)cc(-c2cccc(C(=O)N(C)C)c2)c1N=C(O)c1cnn2cccnc12
106544069
CC1CCN(CCN=C(O)N[C@H](CN2CCCC2=O)c2ccccc2)CC1
109313289
O=C(O)[C@@H]1O[C@H](O[C@@H](CC[C@@H]2C(=O)N(c3ccc(F)cc3)[C@H]2c2ccc(O)cc2)c2ccc(F)cc2)[C@H](O)[C@H](O)[C@@H]1O
136523734
COc1ccccc1CC(=O)Nc1ccc(-n2cc(CO)nn2)cc1
MCULE-1743224427
COC(=O)c1sc(N=C(O)CCC(O)=Nc2ccccc2C(F)(F)F)nc1C
175282547
C=C(/C=C\C(=C)C(C)CCC(C)C)B(O)O
120244794
CCCNc1nccnc1-c1cc(Br)ccc1Cl
23938150
Cc1ccc(N=C(O)N2CCCC2c2ccccc2F)cc1F
169076769
C=CCOc1ccc(C2N=C(S)Nc3nc(S)nc(S)c32)c(OCC=C)c1
145532047
Cc1ncoc1-c1nnc(SCCCN2CC[C@@]3(C[C@@H]3c3ccc(F)cc3)C2)n1C.Cl
137878940
CCc1oc(C(=O)OC)cc1COc1cc(Cl)ccc1C(=N)O
96897682
CC(C)C[C@H](NS(=O)(=O)c1cccc2c(N(C)C)cccc12)C(O)=N[C@@H](CCCNC(=N)N)C(=O)O
33232781
C[C@H](N=C(O)OCc1ccccc1)C(=O)OCC(F)(F)F
47666425
Fc1ccccc1N=C(S)NC1C2CC3CC(C2)CC1C3
126452137
CN(Cc1ccccc1C(F)(F)F)C(=O)CCc1ccc2[nH]ccc2c1
27432563
CN(C)c1ccc2coc(-c3ccc(N4C(=O)C=CC4=O)cc3)c2c1
101263430
COc1ccc(C(Nc2ccn(CC[C@H](CP(=O)(OC)OC)OC(=O)[C@H](Cc3ccccc3)OC)c(=O)n2)(c2ccccc2)c2ccccc2)cc1
158371727
C[C@H](c1noc([C@H]2C[C@@H]2c2ccc(C#N)cc2)n1)C1CC1
100715528
COc1c(N=C(O)Nc2ccc(Oc3ccnc(Nc4ccccc4)c3)c3ccccc23)cc(C(C)(C)C)cc1C(O)=NCCN1CCNCC1
60362823
ClC=CC1CCCCC1
22273455
CCCS(=O)(=O)Nc1cccc(NC(=O)c2ccc(OCC)cc2)c1C
53803853
Cc1ccccc1-c1noc(CN2CCCC(C(O)=Nc3cccc([N+](=O)[O-])c3C)C2)n1
163412875
COc1cc2c(cc1OC)CN(C(=O)c1ccccc1N=C(O)N1CC3C[C@H](C1)Cn1c3cccc1=O)CC2
MCULE-3413055468
CCN(CC)c1ccc(C2C(C(=O)c3cccc(Cl)c3)=C(O)C(=O)N2C(C)C)cc1
MCULE-4221526941
COc1cc(N=C(O)c2cc(F)cc(F)c2)cc(-c2cncc(C)c2)c1
98274462
N=C(N)NCCC[C@@H]1N[C@H](CN=C(O)C=Cc2c(F)cccc2F)CCN(CC(c2ccccc2)c2ccccc2)C1=O
140093626
Cc1nc(-c2ncccn2)nc(O)c1CC(=O)N(Cc1ccccc1F)C1CC1
MCULE-1169132047
CCOc1ccc(-c2ccc(C(=O)N3CCC(F)C3)cc2)c(C)c1
152978446
COc1cccc(N=C(O)[C@@H](OC(=O)c2cccc(C)c2)[C@@H](OC(=O)c2cccc(C)c2)C(=O)O)c1
60613851
C[C@@H](C(=O)[NH2+]c1ccc([N+](=O)[O-])cc1)N1CCN(CCO)CC1
79694221
CCCCCCCC/C=C\CCCCCCCCCCCC(=O)CCCCCCCCCCCCCCC(O)=N[C@@H](CO)CCCCCCCCCCCCCCCC
47641181
Cc1ccc(S(=O)(=O)NN=C(O)[C@H]2[C@@H](C(=O)O)[C@H]3C=C[C@@H]2C3)cc1
148835435
CCOC(=O)c1cc(Cc2cccs2)ncn1
MCULE-8983253583
CC(C)c1c(C(C)(C)C)nn(Cc2c(O)cccc2F)c1I
63837265
CN(CC(O)=Nc1cccc(F)c1)Cc1cc(-c2cccs2)on1
60632034
C1O[C@H]1CN1CC[NH+](C[C@H]2CO2)CC1
MCULE-4000818613
CCOc1ncccc1-c1c(C)cccc1N=C(O)c1ccc(OC)cc1OC
MCULE-4178366139
CCCN(CCC(=O)OCC)c1cc(N2CCN(C(c3ccccc3)c3ccccc3)CC2)nc(C(C)C)n1
23853900
NCCSCc1nc(O)c2ccc(Cl)cc2n1
143225786
COC(=O)c1ccc(NC(=O)c2cc(C)nc(C(F)(F)F)n2)cc1F
97590527
CC(C)CC(N=C(O)Cc1cccs1)C(O)CN=C(O)c1ccc2c(c1)OCO2
End of preview. Expand in Data Studio

MolPILE dataset

ArXiv preprint: "MolPILE - large-scale, diverse dataset for molecular representation learning" J. Adamczyk, J. Poziemski, F. Job, M. Król, M. Makowski

GitHub repository: https://github.com/scikit-fingerprints/MolPILE_dataset

Description

MolPILE is a large-scale molecular dataset designed for pretraining and evaluating machine learning models in cheminformatics. It is compiled from several major chemical databases: UniChem, PubChem, Mcule, ChemSpace, SuperNatural3, and COCONUT. Workflow included preprocessing, standardization, and feasibility filtering of molecules.

Data dictionary

Columns and meaning:

  • source

    Source dataset identifier. Combined with id column, it provides full traceability to the original data entry.

    Possible values: PubChem, UniChem, Mcule, ChemSpace, SuperNatural3, COCONUT

  • id

    A unique identifier for the molecule, retained from its source database (e.g., Mcule ID, PubChem CID).

    Example: MCULE-7212330550

  • SMILES:

    Canonical SMILES representation of the molecule, after RDKit processing.

    Example: O=C(O)C1=CC=CC(O)C1O

Statistics

Descriptor Value
Molecules count 221,950,487
Median SAScore 3.05
#Circles 6,422,057
Bemis-Murcko scaffolds 3,620,809
Ertl functional groups 128,347
Salts 1,089,501

Workflow

MolPILE Workflow

Loading the MolPILE dataset

import polars as pl
from huggingface_hub import hf_hub_download

parquet_file_path = hf_hub_download(
    repo_id="scikit-fingerprints/MolPILE",
    repo_type="dataset",
    filename="molpile.parquet",
    local_dir="datasets",
    local_dir_use_symlinks=False
)

df = pl.read_parquet(parquet_file_path)
print(df.head())

Licenses

MolPILE is a collection of processed datasets, not a single dataset. It is shared as a single Parquet file only for convenience. Individual sources are separated by source and id columns. Each source has its own separate license, which we list below. As its entirety, MolPILE does not have a single license, as it is a collection, not a single dataset. Users interested in that can easily filter the dataset by source. In case of PubChem and UniChem, users may also want to check the individual licenses of their sources. Users using those sources are also asked to cite the appropriate publications, which we provide below. We do not make any claims about licensing of models trained on MolPILE, nor put any additional limitations.

  • UniChem: CC0 (public domain); Chambers, Jon, et al. "UniChem: a unified chemical structure cross-referencing and identifier tracking system." Journal of Cheminformatics 5.1 (2013): 3.
  • PubChem: CC-BY-4.0; Kim, Sunghwan, et al. "PubChem 2023 update." Nucleic Acids Research 51.D1 (2023): D1373-D1380.
  • Mcule: CC-BY-NC-4.0; Kiss, Robert, Mark Sandor, and Ferenc A. Szalai. "http://Mcule.com: a public web service for drug discovery." Journal of Cheminformatics 4.Suppl 1 (2012): P17.
  • ChemSpace: CC-BY-NC-4.0; please cite link https://chem-space.com/compounds/screening-compound-catalog
  • SuperNatural3: not specified, only "freely available"; Gallo, Kathleen, et al. "SuperNatural 3.0 - a database of natural products and natural product-based derivatives." Nucleic Acids Research 51.D1 (2023): D654-D659.
  • COCONUT: CC0 (public domain); Sorokina, Maria, et al. "COCONUT online: collection of open natural products database." Journal of Cheminformatics 13.1 (2021): 2.
Downloads last month
141