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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 list of items that form a dataset with actual data being stored in subdirectories.

Note that *.ds files may contain only subsets of PDB files in individual directories (e.g. holo4k.ds).


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 bound state
  • FPTRAIN: dataset used by Fpocket for training its pocket scoring function
  • HOLO4K: large dataset of protein-ligand complexes. Contains larger multi chain structures downloaded directly from PDB. Disjunct with CHEN11 and JOINED.


  • "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 subset of original dataset for which given method finished successfully and produced predictions (mp: MetaPocket2, sh: SiteHound, ds: DeepSite)


This repository also contains binding site predictions prodused 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 ../ -i {} -p CMET -k (executed in 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


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


Datasets for P2Rank project.



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