Peptide Properties · LiteFold
CycPepMPDB
Curated experimental membrane permeability measurements and structural data for cyclic peptides.
What CycPepMPDB is
CycPepMPDB (Cyclic Peptide Membrane Permeability Database, or CycPeptMPDB) is a database of experimentally measured membrane permeability values for cyclic peptides. Originally developed by Yutaka Akiyama and colleagues at the Tokyo Institute of Technology, it compiles experimental records from published literature and pharmaceutical patents to support computational modeling.
Cyclic peptides are an established modality for targeting intracellular sites such as protein-protein interfaces, but poor passive membrane permeability remains a primary obstacle to therapeutic development. CycPepMPDB addresses the historical absence of unified training and benchmarking resources by providing harmonised permeability data alongside structural annotations.
The core collection incorporates 7,334 cyclic peptides drawn from 45 journal articles and two pharmaceutical patents. Over 99% of the molecules contain non-natural chemical building blocks, such as D-amino acids, N-methylated residues, and modified backbones, which are catalogued alongside multi-assay permeability values, 2D structures, and 3D conformers.
How it was made
Permeability measurements are compiled from disparate primary sources, covering parallel artificial membrane permeability assays (PAMPA), Caco-2 cell monolayers, and MDCK or RRCK cell lines, and converted into harmonised numerical units. Chemical identities are encoded as SMILES strings, 3D conformers, and Hierarchical Editing Language for Macromolecules (HELM) sequences, which standardise the representation of non-natural residues and cyclised backbones.
In this tabular release, records are divided into training (7,983 rows) and testing (868 rows) sets using a deterministic hash assignment: sha256(record_id) % 10, allocating bucket 0 to testing and buckets 1 to 9 to training. Entries contain source provenance fields, entity labels indicating peptide or monomer status, assay names, target annotations, and molecular descriptor columns.
Key facts
- Curated peptides
- 7,334 cyclic peptides
- Original sources
- 45 published papers and 2 pharmaceutical patents
- Permeability assays
- PAMPA, Caco-2, MDCK, and RRCK
- Structural representations
- HELM, SMILES, 2D structures, and 3D conformer coordinates
- Data format
- Parquet tabular dataset
- Release year
- 2023
What you can use it for
- Permeability regression modeling
- Training chemoinformatics models and graph neural networks to predict quantitative membrane permeability from cyclic peptide chemical structures.
- Sequence-based language modeling
- Training sequence models on HELM or SMILES strings to evaluate how non-natural amino acid substitutions influence cellular transport.
- 3D conformer ensemble analysis
- Investigating the influence of three-dimensional molecular conformation and spatial shielding on passive membrane permeation.
- Assay-specific benchmark evaluation
- Benchmarking predictive algorithm performance across artificial membrane systems like PAMPA versus cellular transport assays like Caco-2.
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How the columns are distributed
Over 7,983 rows of default/train
assay_name
string_label- CycPeptMPDB_Peptide_All96%
- CycPeptMPDB_Monomer_All4%
balabanj
string_text- min
- 8
- median
- 11
- mean
- 10.91
- max
- 11
bcut2d_chghi
string_label- -3.15e-162%
- -3.09e-162%
- -2.82e-162%
bcut2d_chglo
string_text- min
- 9
- median
- 12
- mean
- 11.92
- max
- 12
bcut2d_logphi
string_label- -2.52e-162%
- -2.57e-161%
- -3.61e-161%
bcut2d_logplow
string_text- min
- 9
- median
- 12
- mean
- 11.86
- max
- 12
bcut2d_mrhi
string_text- min
- 3
- median
- 9
- mean
- 8.64
- max
- 23
bcut2d_mrlow
string_text- min
- 8
- median
- 12
- mean
- 11.90
- max
- 12
bcut2d_mwhi
string_text- min
- 3
- median
- 8
- mean
- 8.10
- max
- 11
bcut2d_mwlow
string_label- -0.24928776730%
- -0.24928776914%
- -0.24928776213%
bertzct
string_text- min
- 8
- median
- 11
- mean
- 10.86
- max
- 11
caco2
string_label- -5.961%
- -5.890%
- -5.920%
85.0% empty
capped_smiles
string_label- CN[C@@H](C=O)CC(C)C0%
- CCC[C@H](C)[C@@H](OC)[C@@H](C)[C@H](C/C=C(\C)C=O)OC0%
- CN[C@H](C=O)COCC(C)(C)O0%
95.6% empty
chcl3_3dpsa
string_label- 117.01%
- 121.01%
- 114.01%
15.6% empty
chi0
string_text- min
- 9
- median
- 11
- mean
- 10.79
- max
- 11
chi0n
string_text- min
- 9
- median
- 11
- mean
- 10.71
- max
- 11
chi0v
string_text- min
- 8
- median
- 11
- mean
- 10.72
- max
- 11
chi1
string_text- min
- 9
- median
- 11
- mean
- 10.93
- max
- 11
chi1n
string_text- min
- 9
- median
- 11
- mean
- 10.96
- max
- 11
chi1v
string_text- min
- 9
- median
- 11
- mean
- 10.95
- max
- 11
chi2n
string_text- min
- 9
- median
- 11
- mean
- 10.94
- max
- 11
chi2v
string_text- min
- 9
- median
- 11
- mean
- 10.95
- max
- 11
chi3n
string_text- min
- 3
- median
- 11
- mean
- 10.75
- max
- 11
chi3v
string_text- min
- 3
- median
- 11
- mean
- 10.75
- max
- 11
chi4n
string_text- min
- 3
- median
- 11
- mean
- 10.87
- max
- 11
chi4v
string_text- min
- 3
- median
- 11
- mean
- 10.87
- max
- 11
compound_name
string_label- N.D2%
- N-methyl-N6-methyl-L-lysine0%
- D-asparagine0%
95.6% empty
contain_count
string_label- ['1', '0', '0', '0', '0', '0']1%
- ['4', '0', '0', '0', '0', '0']0%
- ['2', '0', '0', '0', '0', '0']0%
95.6% empty
contain_id
string_label- []0%
- [959]0%
- [964]0%
95.6% empty
contain_pepnum
string_label- 11%
- 40%
- 20%
95.6% empty
contain_perme
string_label- [0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0]0%
- [0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0]0%
- [0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0]0%
95.6% empty
cxsmiles
string_label- CC(C)(O)COC[C@H](N[*])C([*])=O |$;;;;;;;;;_R1;;_R2;$|0%
- C[C@H](CCCN[*])C([*])=O |$;;;;;;_R1;;_R2;$|0%
- CC(C)(C)NC(=O)[C@H]([C@@H]1CN1[*])N1CCC[C@H]1C([*])=O |$;;;;;;;;;;;_R1;;;;;;;_R2;$|0%
95.6% empty
dataset_id
string_label- cycpeptmpdb100%
detection_limit_1
string_label- 0 (x 10^-6 cm/s) is the value described in the original paper (permeability was set to -10 by CycPeptMPDB)3%
- Although it was not mentioned in the text, it may be -7 (by CycPeptMPDB)0%
- there was no value in original paper (since %T>100, permeability was set to -4 by CycPeptMPDB)0%
95.8% empty
detection_limit_2
string_label- 0 (x 10^-6 cm/s) is the value described in the original paper (permeability was set to -10 by CycPeptMPDB)0%
- < -6.85 (limit of detection issues prevented quantification of the absolute value of the apparent permeabilities)0%
- < -70%
99.6% empty
entity_type
string_label- peptide96%
- monomer4%
epsa
string_label- 74.00%
- 77.00%
- 61.00%
99.3% empty
estate_vsa1
string_text- min
- 8
- median
- 11
- mean
- 10.89
- max
- 11
estate_vsa10
string_label- 23.38506254%
- 24.755821063%
- 4.7945371843%
estate_vsa11
string_label- 28.767223124%
- 33.5617602924%
- 43.1508346618%
estate_vsa2
string_label- 096%
- 0.04%
- 4.977003270%
estate_vsa3
string_label- 096%
- 0.04%
- 11.336785880%
estate_vsa4
string_label- 0100%
estate_vsa5
string_label- 0100%
estate_vsa6
string_label- 0100%
estate_vsa7
string_label- 0100%
estate_vsa8
string_label- 0.047%
- 4.73686295424%
- 5.10880819116%
estate_vsa9
string_label- 87.728547596%
- 61.684135032%
- 57.571859362%
exactmolwt
string_text- min
- 8
- median
- 11
- mean
- 10.97
- max
- 11
fpdensitymorgan1
string_text- min
- 3
- median
- 11
- mean
- 10.20
- max
- 11
fpdensitymorgan2
string_text- min
- 3
- median
- 11
- mean
- 10.13
- max
- 11
fpdensitymorgan3
string_text- min
- 3
- median
- 11
- mean
- 9.99
- max
- 11
fr_al_coo
string_label- 0100%
- 10%
- 40%
fr_al_oh
string_label- 079%
- 120%
- 21%
fr_al_oh_notert
string_label- 0100%
fr_aldehyde
string_label- 096%
- 14%
- 20%
fr_alkyl_carbamate
string_label- 0100%
- 10%
fr_alkyl_halide
string_label- 098%
- 31%
- 21%
fr_allylic_oxid
string_label- 099%
- 10%
- 20%
fr_amide
string_label- 725%
- 624%
- 922%
fr_amidine
string_label- 0100%
fr_aniline
string_label- 0100%
- 10%
fr_ar_coo
string_label- 0100%
fr_ar_n
string_label- 095%
- 12%
- 21%
fr_ar_nh
string_label- 099%
- 11%
- 20%
fr_ar_oh
string_label- 097%
- 13%
- 20%
fr_arn
string_label- 0100%
- 10%
fr_aryl_methyl
string_label- 099%
- 11%
fr_azide
string_label- 0100%
fr_azo
string_label- 0100%
fr_barbitur
string_label- 0100%
fr_benzene
string_label- 230%
- 129%
- 028%
fr_benzodiazepine
string_label- 0100%
fr_bicyclic
string_label- 142%
- 229%
- 025%
fr_c_o
string_label- 725%
- 624%
- 1023%
fr_c_o_nocoo
string_label- 725%
- 624%
- 1023%
fr_c_s
string_label- 0100%
- 10%
fr_coo
string_label- 0100%
- 10%
- 40%
fr_coo2
string_label- 0100%
- 10%
- 40%
fr_diazo
string_label- 0100%
fr_dihydropyridine
string_label- 0100%
fr_epoxide
string_label- 0100%
fr_ester
string_label- 080%
- 120%
- 20%
fr_ether
string_label- 066%
- 129%
- 23%
fr_furan
string_label- 0100%
- 10%
fr_guanido
string_label- 0100%
- 10%
- 30%
fr_halogen
string_label- 094%
- 13%
- 21%
fr_hdrzine
string_label- 0100%
fr_hdrzone
string_label- 0100%
fr_hoccn
string_label- 0100%
- 10%
fr_imidazole
string_label- 0100%
- 10%
fr_imide
string_label- 0100%
- 30%
fr_imine
string_label- 0100%
- 10%
- 20%
fr_isocyan
string_label- 0100%
fr_isothiocyan
string_label- 0100%
fr_ketone
string_label- 0100%
- 10%
fr_ketone_topliss
string_label- 0100%
- 10%
fr_lactam
string_label- 0100%
fr_lactone
string_label- 083%
- 117%
- 20%
fr_methoxy
string_label- 099%
- 11%
- 20%
fr_morpholine
string_label- 099%
- 11%
fr_n_o
string_label- 0100%
fr_ndealkylation1
string_label- 124%
- 220%
- 314%
fr_ndealkylation2
string_label- 063%
- 137%
- 20%
fr_nh0
string_label- 423%
- 519%
- 314%
fr_nh1
string_label- 427%
- 323%
- 220%
fr_nh2
string_label- 099%
- 11%
- 20%
fr_nhpyrrole
string_label- 099%
- 11%
- 20%
fr_nitrile
string_label- 0100%
fr_nitro
string_label- 0100%
- 10%
fr_nitro_arom
string_label- 0100%
- 10%
fr_nitro_arom_nonortho
string_label- 0100%
fr_nitroso
string_label- 0100%
fr_oxazole
string_label- 0100%
- 10%
fr_oxime
string_label- 0100%
fr_para_hydroxylation
string_label- 099%
- 11%
- 20%
fr_phenol
string_label- 097%
- 13%
- 20%
fr_phenol_noorthohbond
string_label- 097%
- 13%
- 20%
fr_phos_acid
string_label- 0100%
fr_phos_ester
string_label- 0100%
fr_piperdine
string_label- 081%
- 119%
- 20%
fr_piperzine
string_label- 0100%
fr_priamide
string_label- 099%
- 11%
- 20%
fr_prisulfonamd
string_label- 0100%
fr_pyridine
string_label- 099%
- 11%
fr_quatn
string_label- 0100%
fr_sh
string_label- 0100%
fr_sulfide
string_label- 097%
- 13%
fr_sulfonamd
string_label- 0100%
- 10%
fr_sulfone
string_label- 0100%
- 10%
fr_term_acetylene
string_label- 0100%
fr_tetrazole
string_label- 0100%
- 10%
fr_thiazole
string_label- 099%
- 11%
- 20%
fr_thiocyan
string_label- 0100%
fr_thiophene
string_label- 0100%
- 10%
fr_unbrch_alkane
string_label- 0100%
fr_urea
string_label- 0100%
fractioncsp3
string_label- 0.8076923085%
- 0.8113207554%
- 0.8039215694%
h2o_3dpsa
string_label- 118.01%
- 119.01%
- 116.01%
15.6% empty
hallkieralpha
string_label- -5.316%
- -5.2710%
- -4.499%
heavyatomcount
string_label- 725%
- 565%
- 574%
heavyatommolwt
string_text- min
- 5
- median
- 7
- mean
- 7.14
- max
- 8
helm
string_text- min
- 55
- median
- 89
- mean
- 91.88
- max
- 171
4.4% empty
helm_url
string_text- min
- 135
- median
- 292
- mean
- 333.72
- max
- 568
4.4% empty
id
string_text- min
- 1
- median
- 4
- mean
- 3.82
- max
- 4
ipc
string_text- min
- 5
- median
- 8
- mean
- 11.93
- max
- 23
iupac_condensed
string_label- N.D2%
- Me-D-Leu-OH0%
- H-Nva-OH0%
95.6% empty
iupac_name
string_label- N.D0%
- (2S)-2-amino-3-(2-hydroxy-2-methylpropoxy)propanoic acid0%
- (2R)-4-methyl-2-(methylamino)pentanoic acid0%
95.6% empty
kappa1
string_text- min
- 8
- median
- 11
- mean
- 10.89
- max
- 11
kappa2
string_text- min
- 4
- median
- 11
- mean
- 10.91
- max
- 11
kappa3
string_text- min
- 3
- median
- 11
- mean
- 10.80
- max
- 11
label
string_label- Circle63%
- Lariat33%
4.4% empty
labuteasa
string_text- min
- 9
- median
- 11
- mean
- 10.94
- max
- 11
maxabsestateindex
string_text- min
- 3
- median
- 11
- mean
- 10.87
- max
- 11
maxabspartialcharge
string_label- 0.45837509810%
- 0.3907167557%
- 0.4583749526%
maxestateindex
string_text- min
- 3
- median
- 11
- mean
- 10.87
- max
- 11
maxpartialcharge
string_label- 0.32870883610%
- 0.3287088377%
- 0.2456756656%
mdck
string_label- -6.40%
- -6.30%
- -4.40%
99.2% empty
minabsestateindex
string_text- min
- 6
- median
- 11
- mean
- 10.88
- max
- 11
minabspartialcharge
string_label- 0.32870883610%
- 0.3287088377%
- 0.2456756656%
minestateindex
string_text- min
- 7
- median
- 12
- mean
- 11.90
- max
- 12
minpartialcharge
string_label- -0.45837509810%
- -0.3907167557%
- -0.4583749526%
molecule_shape
string_label- Circle63%
- Lariat33%
4.4% empty
mollogp
string_text- min
- 3
- median
- 6
- mean
- 5.87
- max
- 8
molmr
string_text- min
- 5
- median
- 8
- mean
- 7.91
- max
- 8
molwt
string_text- min
- 5
- median
- 7
- mean
- 7.30
- max
- 8
monomer_length
string_label- 625%
- 723%
- 1020%
4.4% empty
monomer_length_in_main_chain
string_label- 738%
- 625%
- 1112%
4.4% empty
monomer_type
string_label- Backbone4%
- Terminal0%
95.6% empty
mutation
string_text- min
- 1
- median
- 4
- mean
- 3.82
- max
- 4
natural_analog
string_label- X1%
- F1%
- G1%
95.6% empty
nhohcount
string_label- 422%
- 321%
- 219%
nocount
string_label- 1427%
- 2021%
- 1215%
null
string_labelNo distribution reported for this column.
100.0% empty
numaliphaticcarbocycles
string_label- 096%
- 13%
- 21%
numaliphaticheterocycles
string_label- 349%
- 239%
- 16%
numaliphaticrings
string_label- 349%
- 237%
- 16%
numaromaticcarbocycles
string_label- 230%
- 129%
- 028%
numaromaticheterocycles
string_label- 095%
- 14%
- 20%
numaromaticrings
string_label- 231%
- 128%
- 027%
numhacceptors
string_label- 728%
- 1119%
- 615%
numhdonors
string_label- 422%
- 321%
- 219%
numheteroatoms
string_label- 1427%
- 2018%
- 1214%
numradicalelectrons
string_label- 0100%
numrotatablebonds
string_label- 178%
- 158%
- 167%
numsaturatedcarbocycles
string_label- 096%
- 13%
- 21%
numsaturatedheterocycles
string_label- 347%
- 240%
- 17%
numsaturatedrings
string_label- 348%
- 238%
- 17%
numvalenceelectrons
string_label- 4085%
- 4144%
- 3104%
original_name_in_source_literature
string_text- min
- 1
- median
- 8
- mean
- 8.39
- max
- 42
4.4% empty
pampa
string_label- -10.03%
- -5.31%
- -7.01%
17.6% empty
pc1
string_text- min
- 9
- median
- 11
- mean
- 11.37
- max
- 12
4.4% empty
pc2
string_text- min
- 8
- median
- 11
- mean
- 11.37
- max
- 12
4.4% empty
peoe_vsa1
string_label- 35.529078988%
- 50.475665028%
- 35.119175367%
peoe_vsa10
string_label- 60.2410502417%
- 36.1073548114%
- 42.125247288%
peoe_vsa11
string_label- 5.64736831326%
- 4.23552623522%
- 2.82368415719%
peoe_vsa12
string_label- 41.3502581125%
- 35.4430783821%
- 53.1646175621%
peoe_vsa13
string_label- 0.096%
- 1.4311996573%
- 5.9071797290%
peoe_vsa14
string_label- 0.078%
- 5.96930528820%
- 6.1762985171%
peoe_vsa2
string_label- 33.5617602924%
- 43.1508346622%
- 28.767223122%
peoe_vsa3
string_label- 0.077%
- 4.79453718419%
- 4.9839785211%
peoe_vsa4
string_label- 0.097%
- 13.171245141%
- 5.0986818081%
peoe_vsa5
string_label- 0.095%
- 11.761884953%
- 5.0986818081%
peoe_vsa6
string_label- 68.5189211716%
- 71.3234462412%
- 87.8317555510%
peoe_vsa7
string_label- 100.529896816%
- 74.707690977%
- 68.004259885%
peoe_vsa8
string_text- min
- 3
- median
- 11
- mean
- 10.89
- max
- 11
peoe_vsa9
string_label- 13.7075855618%
- 16.449102677%
- 15.078344125%
permeability
string_label- -10.03%
- -5.961%
- -5.891%
4.4% empty
polymer_type
string_label- PEPTIDE4%
95.6% empty
psa
string_label- 255.00%
- 178.00%
- 162.00%
99.2% empty
pubchem_cid
string_label- N.D1%
- 69511230%
- 1424907300%
95.6% empty
qed
string_text- min
- 8
- median
- 11
- mean
- 10.88
- max
- 11
r1
string_label- H4%
- -0%
95.6% empty
r2
string_label- OH4%
- -0%
95.6% empty
r3
string_label- -4%
- H0%
- OH0%
95.6% empty
r_caco2
string_label- 82.00%
- 55.00%
- 63.00%
99.7% empty
r_mdck
string_label- 75.00%
- 80.00%
100.0% empty
r_pamap
string_text- min
- 3
- median
- 5
- mean
- 4.86
- max
- 11
76.6% empty
r_rrck
string_label- 77.840%
- 59.80%
- 47.10%
99.6% empty
raw_sequence
string_text- min
- 20
- median
- 51
- mean
- 57.11
- max
- 133
4.4% empty
record_id
string_text- min
- 64
- median
- 64
- mean
- 64
- max
- 64
replaced_smiles
string_label- CN[C@H](CC(C)C)C(=O)O0%
- CC(C)(O)COC[C@H](N)C(=O)O0%
- CN[C@@H](CCC(N)=O)C(=O)O0%
95.6% empty
ringcount
string_label- 331%
- 428%
- 521%
rrck
string_label- -5.390%
- -7.00%
- -5.310%
97.9% empty
same_peptides_assay
string_label- [['PAMPA']]4%
- [['Caco2']]4%
- [['PAMPA', 'Caco2']]0%
89.8% empty
same_peptides_id
string_label- [7528]0%
- [2142, 7912]0%
- [7514]0%
89.8% empty
same_peptides_permeability
string_label- [['-4.48']]0%
- [['-4.64']]0%
- [['-5.96']]0%
89.8% empty
same_peptides_source
string_label- ['2023_Ohta']4%
- ['2013_CHUGAI']4%
- ['2018_CHUGAI']1%
89.8% empty
score_value
float- min
- -10
- median
- -5.76
- mean
- -5.96
- max
- -3.90
4.4% empty
sequence
string_text- min
- 20
- median
- 51
- mean
- 57.11
- max
- 133
4.4% empty
sequence_length
int- min
- 20
- median
- 51
- mean
- 57.11
- max
- 133
4.4% empty
sequence_logp
string_text- min
- 27
- median
- 129
- mean
- 141.53
- max
- 292
4.4% empty
sequence_tpsa
string_text- min
- 14
- median
- 52
- mean
- 56.75
- max
- 104
4.4% empty
slogp_vsa1
string_label- 21.2392534127%
- 15.9294400622%
- 10.6196267118%
slogp_vsa10
string_label- 0.097%
- 13.171245141%
- 8.7808300951%
slogp_vsa11
string_label- 0.094%
- 5.7495118335%
- 11.499023672%
slogp_vsa12
string_label- 0.092%
- 11.761884953%
- 11.600939893%
slogp_vsa2
string_label- 130.02051755%
- 177.79572185%
- 165.91998525%
slogp_vsa3
string_label- 52.6822347919%
- 39.9346851910%
- 35.140148018%
slogp_vsa4
string_label- 17.6818730626%
- 11.7879153722%
- 29.4697884321%
slogp_vsa5
string_text- min
- 8
- median
- 11
- mean
- 10.92
- max
- 11
slogp_vsa6
string_label- 0.026%
- 60.4241870825%
- 30.2120935423%
slogp_vsa7
string_label- 5.64736831325%
- 4.23552623522%
- 2.82368415720%
slogp_vsa8
string_label- 0.097%
- 10.772448432%
- 10.902924931%
slogp_vsa9
string_label- 0100%
smiles
string_text- min
- 47
- median
- 139
- mean
- 160.21
- max
- 320
4.4% empty
smr_vsa1
string_text- min
- 9
- median
- 11
- mean
- 10.86
- max
- 11
smr_vsa10
string_label- 41.3502581124%
- 35.4430783821%
- 59.1339228517%
smr_vsa2
string_label- 0.076%
- 1.43119965722%
- 2.8623993142%
smr_vsa3
string_label- 35.529078988%
- 30.219265638%
- 45.738802078%
smr_vsa4
string_label- 17.6818730627%
- 11.7879153723%
- 29.4697884321%
smr_vsa5
string_text- min
- 3
- median
- 11
- mean
- 10.86
- max
- 11
smr_vsa6
string_label- 26.9453731710%
- 33.921200078%
- 19.969546277%
smr_vsa7
string_label- 0.026%
- 71.5510900625%
- 35.7755450322%
smr_vsa8
string_label- 0100%
smr_vsa9
string_label- 0.094%
- 5.7495118335%
- 11.499023672%
source
string_label- 2020_Townsend35%
- 2021_Kelly17%
- 2013_CHUGAI10%
4.4% empty
source_file
string_label- peptide/cycpeptmpdb/CycPeptMPDB_Peptide_All.csv96%
- peptide/cycpeptmpdb/CycPeptMPDB_Monomer_All.csv4%
source_row_index
int- min
- 0
- median
- 4,005
- mean
- 4036.48
- max
- 8,465
source_table
string_label- tables/peptide_cycpeptmpdb_CycPeptMPDB_Peptide_All.csv.jsonl96%
- tables/peptide_cycpeptmpdb_CycPeptMPDB_Monomer_All.csv.jsonl4%
split_bucket
int- min
- 1
- median
- 5
- mean
- 4.99
- max
- 9
structurally_unique_id
string_text- min
- 1
- median
- 4
- mean
- 3.82
- max
- 4
4.4% empty
subtask_name
string_label- CycPeptMPDB_Peptide_All96%
- CycPeptMPDB_Monomer_All4%
symbol
string_label- (N->O)xiIle0%
- HOCOCH2_Gly_ol0%
- Mono260%
95.6% empty
t_pampa
string_text- min
- 3
- median
- 5
- mean
- 4.52
- max
- 6
39.6% empty
table_group
string_label- all100%
target
string_label- -10.03%
- -5.961%
- -5.891%
4.4% empty
task_name
string_label- CycPeptMPDB100%
tpsa
string_label- 168.548%
- 244.258%
- 159.757%
version
string_label- 1.088%
- 1.212%
vsa_estate1
string_text- min
- 8
- median
- 11
- mean
- 10.88
- max
- 11
vsa_estate10
string_label- 0.092%
- -2.6286841410%
- -2.6421524570%
vsa_estate2
string_text- min
- 3
- median
- 11
- mean
- 10.89
- max
- 12
vsa_estate3
string_text- min
- 3
- median
- 12
- mean
- 11.73
- max
- 12
vsa_estate4
string_text- min
- 3
- median
- 12
- mean
- 9.82
- max
- 12
vsa_estate5
string_text- min
- 3
- median
- 12
- mean
- 11.66
- max
- 12
vsa_estate6
string_text- min
- 3
- median
- 12
- mean
- 11.85
- max
- 12
vsa_estate7
string_text- min
- 3
- median
- 12
- mean
- 11.87
- max
- 12
vsa_estate8
string_text- min
- 3
- median
- 12
- mean
- 11.89
- max
- 12
vsa_estate9
string_label- 0.098%
- -4.014054270%
- -4.3274673410%
x_3dpsa
string_label- 78.30%
- 77.00%
- 87.40%
99.8% empty
year
string_label- 202036%
- 202118%
- 201310%
4.4% empty
Strengths and limits
Good at
- Harmonises experimental permeability measurements from 45 peer-reviewed publications and two patents into consistent numerical units.
- Employs HELM notation to encode the non-natural building blocks, D-amino acids, and N-methylations present in over 99% of entries.
- Provides multiple data modalities per compound, including 1D sequence representations, 2D chemical topologies, and 3D conformers.
- Supplies a deterministic hash split and explicit source-provenance columns linking each row to its original publication or patent.
Watch out for
- Data originates from diverse assay types (PAMPA, Caco-2, RRCK, and MDCK) that measure distinct transport mechanisms and biological environments.
- The hash-based split divides records randomly rather than by scaffold, which can allow structurally similar peptides into both training and test sets.
Questions
Can I look inside CycPepMPDB without downloading it?
Yes. This page reads its schema, real rows and per-column statistics in the browser, with full-text search and a SQL filter. Nothing is downloaded to your machine.
What licence is CycPepMPDB under?
Its authors declare other. Read the terms on the original page before reusing the data.
Which experimental permeability assays are covered?
The database primarily features PAMPA and Caco-2 permeability data, with additional values from MDCK and RRCK assays where available in the source literature.
How are non-natural residues and complex macrocycles represented?
Molecules are represented using the Hierarchical Editing Language for Macromolecules (HELM) sequence notation and standard SMILES strings, allowing unambiguous encoding of modified backbones, N-methylations, and D-amino acids.
How were the training and test splits defined?
Rows are split deterministically using the formula sha256(record_id) % 10, where bucket 0 forms the test set and buckets 1 through 9 form the training set.
Does the dataset include 3D structural data?
Yes, entries in the resource include 3D conformer information alongside their 2D topologies and sequence representations.
How to cite it
Li, Jianan and Yanagisawa, Keisuke and Sugita, Masatake and Fujie, Takuya and Ohue, Masahito and Akiyama, Yutaka. CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides. Journal of Chemical Information and Modeling 2023, 63 (7), 2240-2250. DOI: 10.1021/acs.jcim.2c01573.
Written from CycPepMPDB's own dataset card. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.