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ah4h/holo-raw datasets for P2Rank May 18, 2018
chen11 datasets for P2Rank May 18, 2018
coach420
fptrain
holo4k datasets for P2Rank May 18, 2018
joined note on faulty file in joined/b210 Jan 9, 2019
speed5ds
README.md
ah4h.holoraw(mlig).ds
ah4h.holoraw.ds datasets for P2Rank May 18, 2018
chen11-fpocket.ds datasets for P2Rank May 18, 2018
chen11.ds datasets for P2Rank May 18, 2018
coach420(mlig)-deepsite.ds datasets for P2Rank May 18, 2018
coach420(mlig)-fpocket.ds datasets for P2Rank May 18, 2018
coach420(mlig)-mpk2.ds
coach420(mlig)-shsubset-sitehound.ds
coach420(mlig)-shsubset.ds
coach420(mlig).ds
coach420-deepsite.ds
coach420-fpocket.ds
coach420-lssubset-lise.ds datasets for P2Rank May 18, 2018
coach420-lssubset.ds
coach420-mpsubset-mpk2.ds
coach420-mpsubset.ds
coach420-p2rank.ds datasets for P2Rank May 18, 2018
coach420-shsubset-sitehound.ds
coach420-shsubset.ds
coach420.ds datasets for P2Rank May 18, 2018
fptrain.ds
holo4k(mlig)-dssubset-deepsite.ds
holo4k(mlig)-dssubset.ds
holo4k(mlig)-fpocket.ds
holo4k(mlig)-mpsubset-mpk2.ds
holo4k(mlig)-mpsubset.ds datasets for P2Rank May 18, 2018
holo4k(mlig)-shsubset-sitehound.ds datasets for P2Rank May 18, 2018
holo4k(mlig)-shsubset.ds datasets for P2Rank May 18, 2018
holo4k(mlig).ds datasets for P2Rank May 18, 2018
holo4k-dssubset-deepsite.ds
holo4k-dssubset.ds datasets for P2Rank May 18, 2018
holo4k-fpocket.ds
holo4k-mpsubset-mpk2.ds datasets for P2Rank May 18, 2018
holo4k-mpsubset.ds datasets for P2Rank May 18, 2018
holo4k-shsubset-sitehound.ds datasets for P2Rank May 18, 2018
holo4k-shsubset.ds
holo4k.ds
joined(mlig)-fpocket.ds
joined(mlig).ds datasets for P2Rank May 18, 2018
joined-fpocket.ds datasets for P2Rank May 18, 2018
joined.ds datasets for P2Rank May 18, 2018
speed5.ds datasets for P2Rank May 18, 2018

README.md

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).

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 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.

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

Predictions

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 ../auto.py -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

modifications

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