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LiteFold
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CycPepMPDB

Tasks:
Other
Languages:
English
Size:
10K<n<100K
Tags:
chemistry
peptides
cyclic-peptides
membrane-permeability
jsonl
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CycPepMPDB / README.md
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metadata 
license: other
pretty_name: CycPepMPDB
size_categories:
  - 10K<n<100K
task_categories:
  - other
language:
  - en
tags:
  - chemistry
  - peptides
  - cyclic-peptides
  - membrane-permeability
  - jsonl

CycPepMPDB

CycPepMPDB cyclic peptide membrane-permeability dataset (monomers and analogs), normalized to newline-delimited JSON with row-level provenance.

Processed and uploaded by the MegaData post-download pipeline (internal repo). Original source: http://cycpeptmpdb.com/.

Statistics

Table files 99
Total rows 43,514
Total bytes 259.87 MiB (272,498,665)

Tables

Table Rows Bytes
peptide_cycpeptmpdb_CycPeptMPDB_Monomer_All.csv.jsonl 385 2.23 MiB
peptide_cycpeptmpdb_CycPeptMPDB_Monomer_Analog_A.csv.jsonl 34 216.30 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Monomer_Analog_C.csv.jsonl 4 22.01 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Monomer_Analog_D.csv.jsonl 6 39.63 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Monomer_Analog_E.csv.jsonl 5 25.48 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Monomer_Analog_F.csv.jsonl 63 364.35 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Monomer_Analog_G.csv.jsonl 47 265.58 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Monomer_Analog_H.csv.jsonl 3 15.38 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Monomer_Analog_I.csv.jsonl 8 46.23 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Monomer_Analog_K.csv.jsonl 13 66.15 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Monomer_Analog_L.csv.jsonl 19 191.37 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Monomer_Analog_M.csv.jsonl 3 15.24 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Monomer_Analog_N.csv.jsonl 7 35.72 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Monomer_Analog_P.csv.jsonl 12 110.07 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Monomer_Analog_Q.csv.jsonl 10 51.57 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Monomer_Analog_R.csv.jsonl 4 20.67 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Monomer_Analog_S.csv.jsonl 29 151.32 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Monomer_Analog_T.csv.jsonl 6 48.74 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Monomer_Analog_V.csv.jsonl 15 84.60 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Monomer_Analog_W.csv.jsonl 8 41.30 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Monomer_Analog_X.csv.jsonl 78 417.57 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Monomer_Analog_Y.csv.jsonl 11 58.28 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Peptide_All.csv.jsonl 8,466 50.54 MiB
peptide_cycpeptmpdb_CycPeptMPDB_Peptide_Assay_Caco2.csv.jsonl 1,332 8.23 MiB
peptide_cycpeptmpdb_CycPeptMPDB_Peptide_Assay_MDCK.csv.jsonl 64 396.71 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Peptide_Assay_PAMPA.csv.jsonl 7,298 43.31 MiB
peptide_cycpeptmpdb_CycPeptMPDB_Peptide_Assay_RRCK.csv.jsonl 186 1.09 MiB
peptide_cycpeptmpdb_CycPeptMPDB_Peptide_Length_10.csv.jsonl 1,777 10.82 MiB
peptide_cycpeptmpdb_CycPeptMPDB_Peptide_Length_11.csv.jsonl 675 4.23 MiB
peptide_cycpeptmpdb_CycPeptMPDB_Peptide_Length_12.csv.jsonl 632 3.98 MiB
peptide_cycpeptmpdb_CycPeptMPDB_Peptide_Length_13.csv.jsonl 234 1.49 MiB
peptide_cycpeptmpdb_CycPeptMPDB_Peptide_Length_14.csv.jsonl 125 825.96 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Peptide_Length_15.csv.jsonl 26 174.11 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Peptide_Length_2.csv.jsonl 4 22.71 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Peptide_Length_3.csv.jsonl 69 387.80 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Peptide_Length_4.csv.jsonl 55 313.75 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Peptide_Length_5.csv.jsonl 88 512.88 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Peptide_Length_6.csv.jsonl 2,167 12.50 MiB
peptide_cycpeptmpdb_CycPeptMPDB_Peptide_Length_7.csv.jsonl 2,071 12.09 MiB
peptide_cycpeptmpdb_CycPeptMPDB_Peptide_Length_8.csv.jsonl 120 730.00 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Peptide_Length_9.csv.jsonl 423 2.57 MiB
peptide_cycpeptmpdb_CycPeptMPDB_Peptide_Shape_Circle.csv.jsonl 5,530 32.46 MiB
peptide_cycpeptmpdb_CycPeptMPDB_Peptide_Shape_Lariat.csv.jsonl 2,936 18.15 MiB
peptide_cycpeptmpdb_CycPeptMPDB_Peptide_Source_2006_Rezai_1.csv.jsonl 10 60.53 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Peptide_Source_2006_Rezai_2.csv.jsonl 11 65.58 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Peptide_Source_2011_White.csv.jsonl 10 60.81 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Peptide_Source_2012_Rand.csv.jsonl 16 95.80 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Peptide_Source_2013_CHUGAI.csv.jsonl 878 5.51 MiB
peptide_cycpeptmpdb_CycPeptMPDB_Peptide_Source_2013_Zaretsky.csv.jsonl 2 11.60 KiB
peptide_cycpeptmpdb_CycPeptMPDB_Peptide_Source_2014_Nielsen.csv.jsonl 4 23.96 KiB
… 49 more table file(s) …

Layout 

.
├── _MANIFEST.json                 # aggregate manifest (per-table counts)
└── tables/<source_slug>.jsonl    # normalized rows (one JSON object per line)

Each line in a tables/*.jsonl file is a JSON object with at least dataset_id, row (the raw upstream row), row_index, and source_file fields, so every row carries its upstream provenance.

Loading 

hf download LiteFold/CycPepMPDB --repo-type dataset --local-dir ./cycpeptmpdb

Programmatic streaming:

import json
from pathlib import Path
from huggingface_hub import snapshot_download

local = snapshot_download(repo_id="LiteFold/CycPepMPDB", repo_type="dataset")
for jsonl in sorted(Path(local, "tables").glob("*.jsonl")):
    with jsonl.open() as f:
        for line in f:
            row = json.loads(line)
            ...  # row["row"] is the upstream record

License

See upstream license at CycPepMPDB.

Citation

Li J, et al. CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides. J. Chem. Inf. Model., 2023.

Provenance

Built from the local manifest entry cycpeptmpdb of manifests/atlas_download_plan.json. Pipeline source: megadata-post normalize --dataset cycpeptmpdb --tables-only.