README.md

metadata

license: cc-by-4.0
task_categories:
  - other
tags:
  - biology
  - protein
  - structure
  - PDB
  - PISCES
  - CullPDB
  - sequence
  - curation
language: en
size_categories:
  - n>1M
dataset_info:
  config_name: default
  features:
    - name: pdb_chain
      dtype: string
    - name: pdb
      dtype: string
    - name: chain
      dtype: string
    - name: sequence
      dtype: string
    - name: len
      dtype: int64
    - name: method
      dtype: string
    - name: resolution
      dtype: float64
    - name: rfac
      dtype: string
    - name: freerfac
      dtype: string
    - name: pc
      dtype: float64
    - name: no_breaks
      dtype: string
    - name: R
      dtype: float64
    - name: source_list
      dtype: string
  splits: null
  num_rows: 4540884
data_paths:
  main_csv: curated_csv/cullpdb_combined_chains.csv
  index_csv: curated_csv/cullpdb_list_fasta_index.csv
  full_list_csv: curated_csv/cullpdb_full_compiled_list.csv
  subsets_dir: curated_csv/subsets
  metadata: curated_csv/dataset_metadata.json

PISCES-CulledPDB — Curated chain CSVs

Curated protein chain tables derived from PISCES/CullPDB-style lists and FASTA files. One row per chain with sequence, metadata, and curation parameters.

Dataset: PRMegathon26/PISCES-CulledPDB

Dataset Summary

Item	Description
Main CSV	curated_csv/cullpdb_combined_chains.csv — single table with 4,540,884 chains (one row per chain).
Subset CSVs	curated_csv/subsets/*.csv — 242 files, one per curation subset (same columns as main).
Index	curated_csv/cullpdb_list_fasta_index.csv — 242 rows; maps subset basenames to list/FASTA paths and parameters.

Data paths (metadata)

Main and index files:

• curated_csv/cullpdb_combined_chains.csv — master chain table
• curated_csv/cullpdb_list_fasta_index.csv — subset index
• curated_csv/cullpdb_full_compiled_list.csv — full compiled list
• curated_csv/subsets/ — directory containing one CSV per subset (242 files)

Subset paths: The full list of subset CSV paths is in curated_csv/dataset_metadata.json (keys data_paths and subset_paths). Use it for programmatic listing or with hf_hub_download(..., filename=path).

Main CSV & Subset CSV — Column definitions

Each chain row has the following columns:

Column	Type	Description
pdb_chain	string/number	PDB chain ID (e.g. 1ABC_A)
pdb	string/number	PDB ID (first 4 chars)
chain	string/number	Chain ID
sequence	string/number	Amino acid sequence (one-letter)
len	string/number	Sequence length
method	string/number	Experimental method (e.g. XRAY, NMR)
resolution	string/number	Resolution in Å (per structure)
rfac	string/number	R-factor
freerfac	string/number	Free R-factor
pc	string/number	Sequence identity cutoff % used for this subset
no_breaks	string/number	Whether chain has no breaks (yes/no)
R	string/number	R-factor cutoff used for this subset
source_list	string/number	Subset list basename (identifies curation parameters)

Subset CSVs use the same schema; each file corresponds to one row in the index (one set of parameters: pc, resolution range, no_breaks, R, Nmethods).

Index CSV — Column definitions

Column	Description
list_basename	Subset list basename
fasta_basename	Corresponding FASTA basename
list_path	Full path to list file
fasta_path	Full path to FASTA file
n_chains	Number of chains in this subset
pc	Sequence identity cutoff %
resolution	Resolution range (e.g. 0.0-2.0)
no_breaks	yes/no
R	R-factor cutoff
Nmethods	Experiment types (e.g. Xray, Xray+EM)

Subset naming

Subset list basenames follow:

cullpdb_pc{pc}_res{min}-{max}_[noBrks_]len40-10000_R{R}_{Nmethods}_..._chains{N}

• pc: sequence identity cutoff (%)
• resolution: Å range (e.g. 0.0–2.0)
• noBrks (optional): no breaks in chain
• R: R-factor cutoff
• Nmethods: Xray, Xray+EM, or Xray+Nmr+EM
• N: number of chains in that subset

Usage

from huggingface_hub import hf_hub_download
import pandas as pd

# Download main CSV (large)
path = hf_hub_download(repo_id="PRMegathon26/PISCES-CulledPDB", filename="curated_csv/cullpdb_combined_chains.csv", repo_type="dataset")
df = pd.read_csv(path)

# Or load a single subset
path = hf_hub_download(repo_id="PRMegathon26/PISCES-CulledPDB", filename="curated_csv/subsets/cullpdb_pc20.0_res0.0-1.0_len40-10000_R0.2_Xray_d2026_01_26_chains314.csv", repo_type="dataset")
df = pd.read_csv(path)

Curation workflow

1. Index: List/FASTA pairs scanned → cullpdb_list_fasta_index.csv
2. Build: For each index row, list and FASTA aligned 1:1 → one chain CSV per subset + combined master CSV
3. Filter/visualize: Optional filtering and summary figures from the master CSV

License

CC BY 4.0 (or as specified in the repo).