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Datasets for P2Rank project

These are datasets used by P2Rank ligand binding site prediction tool for training and evaluation.

Each *.ds file contains a list of items that form a dataset with actual data being stored in subdirectories.

⚠️ Important note

Please note that *.ds files that define the datasets from our papers may contain only subsets of PDB files in individual directories. For example holo4k/ directory contains 4543 pdb files but holo4k.ds contains 4009 lines. For reproducibility, 4009 is the correct number of proteins in the HOLO4K dataset used in P2Rank/PrankWeb papers.

Datasets

Main sets of proteins:

  • CHEN11: a dataset of 251 proteins harboring 476 ligands introduced in LBS prediction benchmarking study
  • ASTEX: Astex Diverse set
  • metapocket2 datasets
    • U/B48: Datasets that contain a set of 48 proteins in a bound and unbound state
    • DT198: a dataset of 198 drug-target complexes
    • B210: a benchmarking dataset of 210 proteins in a bound state
  • FPTRAIN: dataset used by Fpocket for training its pocket scoring function
  • HOLO4K: a large dataset of protein-ligand complexes. Contains larger multi-chain structures downloaded directly from PDB. Disjunct with CHEN11 and JOINED.

Variations

  • "standard" ... 1 column of liganated proteins
  • *(mlig)* datasets: datasets that contain explicitly specified relevant ligands. Valid ligand codes come from MOAD 2013 database. Proteins unknown to MOAD and proteins with conflicting ligand codes (valid&invalid) were removed.
  • datasets with predictions: include predictions by other ligand binding site prediction methods (-fpocket.ds, -sitehound.ds, etc. suffixes)
  • *-XXsubset-* datasets: contain a subset of the original datasets for which the given method finished successfully and produced predictions (mp: MetaPocket2, sh: SiteHound, ds: DeepSite)

Predictions

This repository also contains binding site predictions produced by some other methods.

  • Fpocket
    • used version: v1.0 with default parameters
  • SiteHound
    • used version: version labeled as
    • command used to generate predictions: ls *.pdb | xargs -i python ../auto.py -i {} -p CMET -k (executed in a directory with pdb files)
    • default probe and parameters were used
  • MetaPocket 2.0
    • obtained from MetaPocket 2.0 web server by a Python script in Fall 2017 using default parameters
  • DeepSite
    • obtained from DeepSite web server by a Python script in Fall 2017 using default parameters
  • P2Rank
    • correspond to P2Rank 2.0 with default parameters

modifications

  • 1xgf.pdb removed from holo4k datasets (all UNK groups, no ligands)