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yaofutuuuu
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bioinf595-cyp3a4-som

Tasks:
Tabular Classification
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molecule_id
stringlengths
3
42
smiles
stringlengths
3
226
all_som_atom_indices_0based
stringlengths
1
23
teniposide
COc1cc([C@@H]2c3cc4c(cc3[C@@H](O[C@@H]3O[C@@H]5CO[C@@H](c6cccs6)O[C@H]5[C@H](O)[C@H]3O)[C@H]3COC(=O)[C@H]23)OCO4)cc(OC)c1O
29,31
perphenazine
OCCN1CCN(CCCN2c3ccccc3Sc3ccc(Cl)cc32)CC1
24
antipyrine
Cc1cc(=O)n(-c2ccccc2)n1C
6,7
celecoxib
Cc1ccc(-c2cc(C(F)(F)F)nn2-c2ccc(S(N)(=O)=O)cc2)cc1
25
phenacetin
CCOc1ccc(NC(C)=O)cc1
9
nicardipine
COC(=O)C1=C(C)NC(C)=C(C(=O)OCCN(C)Cc2ccccc2)[C@@H]1c1cccc([N+](=O)[O-])c1
0,27,12
NDMA
CN(C)N=O
3,4
cj_12_458
C=C(C)c1ccc(OC)c(CN[C@H]2C3CCN(CC3)[C@@H]2C(c2ccccc2)c2ccccc2)c1
33,31
abt_438
C[C@@H](C#Cc1ccc(Cc2ccccc2)s1)NC(N)=O
6
methoxychlor_mono_OH
COc1ccc([C@@H](c2ccc(O)cc2)C(Cl)(Cl)Cl)cc1
13,14
ezlopitant
COc1ccc(C(C)C)cc1CN[C@H]1C2CCN(CC2)[C@H]1C(c1ccccc1)c1ccccc1
31
11_oxo_delta8_tetrahydrocannabinol
CCCCCc1cc(O)c2c(c1)OC(C)(C)[C@H]1CC=C(C=O)C[C@H]21
16
GTS-21
COc1ccc(/C=C2\CCCN=C2c2cccnc2)c(OC)c1
21,22
dapsone
Nc1ccc(S(=O)(=O)c2ccc(N)cc2)cc1
0,14
serm_I
Oc1ccc([C@H]2Sc3cc(O)ccc3O[C@H]2c2ccc(OCCN3CCCCC3)cc2)cc1
32,9,28
atrazine
CCNc1nc(Cl)nc(NC(C)C)n1
10,7
diazepam
CN1C(=O)CN=C(c2ccccc2)c2cc(Cl)ccc21
9,12
trazodone
O=c1n(CCCN2CCN(c3cccc(Cl)c3)CC2)nc2ccccn12
0,2,12,22
metolachlor
CCc1cccc(C)c1N(C(=O)CCl)[C@@H](C)COC
18
4_hydroxytamoxifen
CC/C(=C(\c1ccc(O)cc1)c1ccc(OCCN(C)C)cc1)c1ccccc1
16,15
NDEA
CCN(CC)N=O
3,5
3-methylether-estradiol
COc1ccc2c(c1)CC[C@@H]1[C@@H]2CC[C@@]2(C)[C@H](O)CC[C@@H]12
20
haloperidol
O=C(CCCN1CCC(O)(c2ccc(Cl)cc2)CC1)c1ccc(F)cc1
0,2,4,6
fluvastatin
CC(C)n1c(/C=C/[C@H](O)C[C@H](O)CC(=O)O)c(-c2ccc(F)cc2)c2ccccc21
11
laam
CC[C@@H](OC(C)=O)C(C[C@@H](C)N(C)C)(c1ccccc1)c1ccccc1
19,20
lithocholic_acid
C[C@H](CCC(=O)O)[C@H]1CC[C@H]2[C@@H]3CC[C@H]4C[C@H](O)CC[C@]4(C)[C@H]3CC[C@]12C
12
9_cis_retinoic_acid
CC1=C(/C=C/C(C)=C\C=C\C(C)=C\C(=O)O)C(C)(C)CCC1
14
ml_3403
CSc1nc(-c2ccnc(N[C@H](C)c3ccccc3)c2)c(-c2ccc(F)cc2)[nH]1
0,5,6
delavirdine
CC(C)Nc1cccnc1N1CCN(C(=O)c2cc3cc(NS(C)(=O)=O)ccc3[nH]2)CC1
26,29
chlorzoxazone
O=c1[nH]c2cc(Cl)ccc2o1
2
adinazolam
CN(C)Cc1nnc2n1-c1ccc(Cl)cc1C(c1ccccc1)=NC2
22,23
triazolam
Cc1nnc2n1-c1ccc(Cl)cc1C(c1ccccc1Cl)=NC2
11,14
indomethacin_phenethylamide
COc1ccc2c(c1)c(CC(=O)NCCc1ccccc1)c(C)n2C(=O)c1ccc(Cl)cc1
25,26
pioglitazone
CCc1ccc(CCOc2ccc(C[C@H]3SC(=O)NC3=O)cc2)nc1
1
sulfinpyrazone_sulfide
O=C1C(CCSc2ccccc2)C(=O)N(c2ccccc2)N1c1ccccc1
1,18,4,23
mianserin
CN1CCN2c3ccccc3Cc3ccccc3[C@@H]2C1
17,19,1
benzo_a_pyrene
c1ccc2c(c1)cc1ccc3cccc4ccc2c1c34
10,12,14,15,16,18,19
pimozide
O=c1[nH]c2ccccc2n1C1CCN(CCCC(c2ccc(F)cc2)c2ccc(F)cc2)CC1
16
phenytoin
O=C1NC(=O)C(c2ccccc2)(c2ccccc2)N1
13,14,15,16,17,18
methaqualone
Cc1ccccc1-n1c(C)nc2ccccc2c1=O
8
cocaine
COC(=O)[C@H]1[C@H](OC(=O)c2ccccc2)C[C@H]2CC[C@@H]1N2C
3
flucloxacillin
Cc1onc(-c2c(F)cccc2Cl)c1C(=O)N[C@@H]1C(=O)N2[C@@H]1SC(C)(C)[C@@H]2C(=O)O
22
imatinib
Cc1ccc(NC(=O)c2ccc(CN3CCN(C)CC3)cc2)cc1Nc1nccc(-c2cccnc2)n1
6
quinidine
C=C[C@H]1CN2CC[C@H]1C[C@@H]2[C@@H](O)c1ccnc2ccc(OC)cc12
12,14
flunitrazepam
CN1C(=O)CN=C(c2ccccc2F)c2cc([N+](=O)[O-])ccc21
8,20
1_8_cineole
CC1(C)O[C@]2(C)CC[C@H]1CC2
0,4
compound_1
O=S(=O)(Nc1ccc(CCNC[C@H](O)c2cccnc2)cc1)c1ccc(C2=NC(c3ccc(C(F)(F)F)cc3)=CC2)cc1
0,8
arachidonic_acid
CCCCC/C=C\C/C=C\C/C=C\C/C=C\CCCC(=O)O
5,7,11,14,17
budesonide
CCC[C@@H]1O[C@@H]2C[C@H]3[C@@H]4CCC5=CC(=O)C=C[C@]5(C)[C@H]4[C@H](O)C[C@]3(C)[C@]2(C(=O)CO)O1
27,7
sertraline
CN[C@H]1CC[C@@H](c2ccc(Cl)c(Cl)c2)c2ccccc21
19,7
ecabapide
CNC(=O)c1cccc(NCC(=O)NCCc2ccc(OC)c(OC)c2)c1
22,14
CP_125_611
Oc1ccc(OC(F)(F)F)cc1CN[C@@H]1CCCN[C@H]1c1ccccc1
16,7
cqa_206_291
CCN(CC)S(=O)(=O)N[C@H]1C[C@@H]2c3cccc4c3c(cn4CC)C[C@H]2N(C)C1
24,25
fipronil
N#Cc1nn(-c2c(Cl)cc(C(F)(F)F)cc2Cl)c(N)c1[S@+]([O-])C(F)(F)F
16,18
propafenone
CCCNC[C@H](O)COc1ccccc1C(=O)CCc1ccccc1
22
MDA
C[C@@H](N)Cc1ccc2c(c1)OCO2
11
7-hexoxycoumarin
CCCCCCOc1ccc2ccc(=O)oc2c1
8,4,6,7
testosterone
C[C@]12CC[C@H]3[C@@H](CCC4=CC(=O)CC[C@@]43C)[C@@H]1CC[C@@H]2O
0,6,14,15,16,19
cyclobenzaprine
CN(C)CCC=C1c2ccccc2C=Cc2ccccc21
19,20
prostaglandin_H2
CCCCC[C@H](O)/C=C/[C@@H]1[C@@H](C/C=C\CCCC(=O)O)[C@@H]2C[C@H]1OO2
8,7
brotizolam
Cc1nnc2n1-c1sc(Br)cc1C(c1ccccc1Cl)=NC2
0,5
NNK
CN(CCCC(=O)c1cccnc1)N=O
10,2
acetochlor
CCOCN(C(=O)CCl)c1c(C)cccc1CC
16
fk_506
C=CC[C@@H]1/C=C(\C)C[C@H](C)C[C@H](OC)[C@H]2O[C@@](O)(C(=O)C(=O)N3CCCC[C@H]3C(=O)O[C@H](/C(C)=C/[C@@H]3CC[C@@H](O)[C@H](OC)C3)[C@H](C)[C@@H](O)CC1=O)[C@H](C)C[C@@H]2OC
10
ebastine
CC(C)(C)c1ccc(C(=O)CCN2CCC(OC(c3ccccc3)c3ccccc3)CC2)cc1
20
lisofylline
C[C@@H](O)CCCCn1c(=O)c2c(ncn2C)n(C)c1=O
16,17
mirtazapine
CN1CCN2c3ncccc3Cc3ccccc3[C@H]2C1
8,17,14
quinoline
c1ccc2ncccc2c1
3,4,5,6,7
territrem_A
COc1cc(-c2cc3c(c(=O)o2)C[C@]2(O)[C@@]4(C)C(=O)C=CC(C)(C)[C@]4(O)CC[C@@]2(C)O3)cc2c1OCO2
35,36
uk_343664
CCCOc1ccc(S(=O)(=O)N2CCN(CC)CC2)cc1-c1nc2c(CC)n(Cc3ccccn3)nc2c(=O)[nH]1
30
6_methylchrysene
Cc1cc2c3ccccc3ccc2c2ccccc12
10,12,13,15,17
NNAL
CN(CC[C@H](O)C(=O)c1cccnc1)N=O
2,11
all_trans_retinal
CC1=C(/C=C/C(C)=C/C=C/C(C)=C/C=O)C(C)(C)CCC1
6
caffeine
Cn1c(=O)c2c(ncn2C)n(C)c1=O
10
ellipticine
Cc1c2ccncc2c(C)c2c1[nH]c1ccccc12
17,11,13,9
terbuthylazine
CCNc1nc(Cl)nc(NC(C)(C)C)n1
7
oxycodone
COc1ccc2c3c1O[C@H]1C(=O)CC[C@@]4(O)[C@@H](C2)N(C)CC[C@]314
21
clotiazepam
CCc1cc2c(s1)N(C)C(=O)CN=C2c1ccccc1Cl
18,11
org_30659
C#C[C@]1(O)C=C[C@H]2[C@@H]3CCC4=CC(=O)CC[C@H]4[C@H]3C(=C)C[C@@]21C
16
erythromycin
CC[C@H]1OC[C@H](C)[C@@H](O[C@H]2C[C@@](C)(OC)[C@@H](O)[C@H](C)O2)[C@H](C)[C@@H](O[C@@H]2O[C@H](C)C[C@H](N(C)C)[C@H]2O)[C@](C)(O)C[C@@H](C)C[C@H](C)[C@@H](O)[C@]1(C)O
48,47
cyamemazine
C[C@H](CN(C)C)CN1c2ccccc2Sc2ccc(C#N)cc21
5,6,7,8,10,21,22
simvastatin
CCC(C)(C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)[C@H]21
21,19,20,13
phenanthrene
c1ccc2c(c1)ccc1ccccc12
3,4,6,7,8,9,10,11,12,13
delta9_tetrahydrocannabinol
CCCCCc1cc(O)c2c(c1)OC(C)(C)[C@H]1CCC(C)=C[C@H]21
8,3,15
pranidipine
COC(=O)C1=C(C)NC(C)=C(C(=O)OC/C=C/c2ccccc2)[C@H]1c1cccc([N+](=O)[O-])c1
0,12
7-benzyloxyresorufin
O=c1ccc2nc3ccc(OCc4ccccc4)cc3oc-2c1
16
acetaminophen
CC(=O)Nc1ccc(O)cc1
0,2
CP_122_721
COc1ccc(OC(F)(F)F)cc1CN[C@@H]1CCCN[C@H]1c1ccccc1
7
2-acetylbenzothiophene
CC(=O)c1cc2ccccc2s1
4
diclofenac
O=C(O)Cc1ccccc1Nc1c(Cl)cccc1Cl
12
laquinimod
CCN(C(=O)c1c(O)c2c(Cl)cccc2n(C)c1=O)c1ccccc1
8,11,12,5
NMBA
CCCCN(C)N=O
3,4
2-2prime-4-5-5prime-pentachlorobiphenyl
Clc1ccc(Cl)c(-c2cc(Cl)c(Cl)cc2Cl)c1
13
zatosetron
CN1[C@@H]2CC[C@H]1C[C@@H](NC(=O)c1cc(Cl)cc3c1OC(C)(C)C3)C2
20,23
sertindole
O=C1NCCN1CCN1CCC(c2cn(-c3ccc(F)cc3)c3ccc(Cl)cc23)CC1
21
7-hydroxy-delta_8_tetrahydrocannabinol
CCCCCc1cc(O)c2c(c1)OC(C)(C)[C@@H]1[C@@H](O)C=C(C)C[C@@H]21
13
pimobendan
COc1ccc(-c2nc3cc(C4=NNC(=O)C[C@@H]4C)ccc3[nH]2)cc1
7
trans_phenylpropene
C/C=C/c1ccccc1
8,6,7
imidacloprid
O=[N+]([O-])/N=C1\NCCN1Cc1ccc(Cl)nc1
7
etoposide
COc1cc([C@@H]2c3cc4c(cc3[C@H](O[C@H]3O[C@H]5CO[C@@H](C)O[C@@H]5[C@@H](O)[C@H]3O)[C@H]3COC(=O)[C@H]23)OCO4)cc(OC)c1O
28,29
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CYP3A4 SoM prediction model

  1. Retrieve 'molecule_id, smiles, SOM_atom_indices' of 3A4 from Zaretzki's data set

    • Successfully created data file:
      /nfs/turbo/dcmb-class/bioinf595/sec001/fuyao/project/intermediate_data/3A4_SOM.csv
    • Total molecules processed: 475

  2. Sanitize molecules

  3. Split dataset into train, valid, and test set

    • Total molecules: 475
    • Train molecules: 285
    • Validation molecules: 95
    • Test molecules: 95

  4. Generate descriptors for each set
    Reference:
    Kirchmair J, Williamson MJ, Afzal AM, Tyzack JD, Choy AP, Howlett A, Rydberg P, Glen RC.
    FAst MEtabolizer (FAME): A rapid and accurate predictor of sites of metabolism in multiple species by endogenous enzymes.
    J Chem Inf Model. 2013 Nov 25;53(11):2896-907.

    Descriptors:

    • gasteiger_charge : atom’s electrostatic potential
    • atomic_num : number of protons
    • hybridization
    • is_aromatic : whether the atom is part of aromatic ring system
    • max_topo_dist : maximum shortest distance between atom and any others

    Hybridization needs to be one-hot encoded to be compatible with tree-based models

  5. H2O model training

    • Result file:
      /nfs/turbo/dcmb-class/bioinf595/sec001/fuyao/project/product/result.txt
    • Best model:
      /nfs/turbo/dcmb-class/bioinf595/sec001/fuyao/project/product/StackedEnsemble_BestOfFamily_1_AutoML_1_20250420_145607
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Number of rows:
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