| --- |
| 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](https://github.com/) 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 |
|
|
| ```bash |
| hf download LiteFold/CycPepMPDB --repo-type dataset --local-dir ./cycpeptmpdb |
| ``` |
|
|
| Programmatic streaming: |
|
|
| ```python |
| 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`. |
|
|
