OncoPPIs-pocketome Repository

A freely available pockets collection named OncoPPIs-pocketome was built to collect the potential binding sites on Protein-Protein Interaction targets, activated under Cancer condition. We provide all 3D protein structures, pockets, and interactors. Three distinct pocket types were identified: 248 interface, 2552 allosteric-like, and 874 equilibrium pockets.
An interface pocket is defined by residues of one partner, and contains residues of the other partner. All the other pockets detected on one partners and not corresponding to interface regions were annotated as allosteric-like pockets. An equilibrium pocket is defined by residues of both partners.

Notably, this work provides, for the first time, a comprehensive reference dataset of protein and pocket structures, accessible to the scientific community for further drug design studies. Additionally, this research introduces a flexible framework for systematically assessing and ranking emerging disease targets, enabling the identification of critical proteins in diseases and offering a structured approach to their evaluation.

1. FILES This directory contains .pdb files of proteins, pockets and ligands. There are two directories:

   • DETACHED: containing detached partners and interface and allosteric-like pockets

     • DETACHED-PARTNER1 contains the first partner and corresponding pockets
     • DETACHED-PARTNER2 contains the second partner and corresponding pockets

   • COMPLEXED: containing complexed partners and equilibrium pockets

   • In each directory of DETACHED-PARTNER1

     • P1_UNIPROT1-UNIPROT2-PDB-chainP1.pdb: protein1
     • P2_UNIPROT1-UNIPROT2-PDB-chainP2.pdb: interactor protein2
     • Pocket_*_P1_UNIPROT1-UNIPROT2-PDB-chainP1.pdb: Pocket shapes generated by detached partner 1
     • PocRes_*_P1_UNIPROT1-UNIPROT2-PDB-chainP1.pdb: Pocket residues

   • In each directory of DETACHED-PARTNER2

     • P2_UNIPROT1-UNIPROT2-PDB-chainP2.pdb: protein2
     • P1_UNIPROT1-UNIPROT2-PDB-chainP1.pdb: interactor protein1
     • Pocket_*_P2_UNIPROT1-UNIPROT2-PDB-chainP2.pdb: Pocket shapes generated by detached partner 2
     • PocRes_*_P2_UNIPROT1-UNIPROT2-PDB-chainP2.pdb: Pocket residues

   • In each directory of COMPLEXED

     • P1P2_UNIPROT1-UNIPROT2-PDB-chainP1P2.pdb: protein complex
     • Pocket_*_P1P2_UNIPROT1-UNIPROT2-PDB-chainP1P2.pdb: Pocket shapes generated by complexed partners
     • PocRes_*_P1P2_UNIPROT1-UNIPROT2-PDB-chainP1P2.pdb: Pocket residues

2. POCKET LIST

   • list_allosteric-like-pockets.csv

   • list_equilibrium_pockets.csv

   • list_interface-pockets.csv

     File containing list of allosteric-like, equilibrium and interface pockets

3. IMPLEMENTATION.txt It contains command lines used for implementing the pocket collection and computing pocket descriptors.The BioGPS software, containing flap* executables is available from https://www.moldiscovery.com/ and trial licenses are available to both commercial and academic users.

4. README.md, This file

---

If you are satisfied, please cite us:

Target Mapping in Cancer: Ligandable Protein Pockets on 3D OncoPPI Networks Trisciuzzi D., Nicolotti O., Cruciani G., Menna G., Siragusa L. Pharmaceuticals 2025, 18(7), 958; https://doi.org/10.3390/ph18070958