Update README.md

README.md

@@ -17,11 +17,11 @@ configs:
     path: data/test-*.parquet
 ---
 
-# LiteFold/CycPepMPDB
+# CycPepMPDB
 
-This repository now includes a Dataset Viewer-friendly Parquet version of the LiteFold CycPepMPDB tables. The default `load_dataset()` configuration reads the normalized Parquet files in `data/`.
+CycPeptMPDB (Cyclic Peptide Membrane Permeability Database) is the standard public dataset of experimentally measured membrane permeability for cyclic peptides, released in 2023 by Akiyama and colleagues at Tokyo Institute of Technology. It exists because cyclic peptides have become a serious modality for hitting "undruggable" intracellular targets like protein-protein interfaces, but their typically poor passive permeability is the bottleneck of the field, and until CycPeptMPDB there was no unified resource to train or benchmark in silico permeability predictors.
+The database aggregates 7,334 cyclic peptides curated from 45 published papers and 2 pharma patents, with experimentally measured permeability values (predominantly PAMPA and Caco-2, also RRCK and MDCK depending on source) under harmonized units. Each entry carries the 2D structure, HELM sequence representation (which cleanly handles the >99% of entries containing non-natural building blocks like N-methylated residues, D-amino acids, and exotic backbones), and 3D conformer data, so the corpus is directly usable for chemoinformatic featurization, graph neural networks, conformational ensemble methods, and language-model approaches over HELM or SMILES. The website at cycpeptmpdb.com adds online visualization, filtering by source assay and scaffold, and bulk downloads. CycPeptMPDB has since become the backbone of essentially all recent cyclic peptide permeability ML work (CycPeptMP and its descendants).
 
-The normalized default table contains 8,851 rows from the `CycPeptMPDB_Peptide_All.csv` and `CycPeptMPDB_Monomer_All.csv` source tables. These all-record tables are used as the default view to avoid duplicating rows from overlapping subset tables. The original wrapped JSONL source tables remain available in the repository under `tables/`.
 
 ## Splits
 
@@ -87,6 +87,18 @@ column_mapping = load_dataset(
 )
 ```
 
-## Rebuild
+# Citation
 
-The normalization script used for this upload is included at `scripts/prepare_wrapped_jsonl_dataset.py`.
+```
+@article{li2023cycpeptmpdb,
+  title     = {{CycPeptMPDB}: A Comprehensive Database of Membrane Permeability of Cyclic Peptides},
+  author    = {Li, Jianan and Yanagisawa, Keisuke and Sugita, Masatake and Fujie, Takuya and Ohue, Masahito and Akiyama, Yutaka},
+  journal   = {Journal of Chemical Information and Modeling},
+  volume    = {63},
+  number    = {7},
+  pages     = {2240--2250},
+  year      = {2023},
+  publisher = {American Chemical Society},
+  doi       = {10.1021/acs.jcim.2c01573}
+}
+```