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Cyclic-peptide - protein complexes benchmark and associated scripts and data


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This is the docking benchmark described in the manuscript: A Cyclisation and Docking Protocol for Cyclic Peptide Modeling using HADDOCK2.4 Vicky Charitou, Siri Camee van Keulen, Alexandre M.J.J. Bonvin


1. Content

In this repository you can find the Dataset directory which contains:

  • 30 XXXX_complex folders listed according to their PDB ID containing the files used for docking
  • 30 XXXX_peptide folders listed according to the complex PDB ID containing:
    • Input peptide conformations for Step 1
    • Output peptide conformations for Step 3 (50 structures)
  • setup-analysis_example.csh A script to run the Fnat (and i-RMSD) analysis

1.1. Each XXXX_complex folder contains:

  • HADDOCK-ready files:

    • XXX_r_b.pdb Bound receptor PDB with renumbered atoms and renamed chain ID
    • XXX_r_u.pdb Unbound receptor PDB with renumbered atoms and renamed chain ID
    • XXX_peptide_XXXw.pdb Bound ligand PDB with renumbered atoms and renamed chain ID
    • ensemble_pdb.list List of all ligand PDBs that are included in the ensemble
  • Distance restraints file:

    • ambig.tbl Ambiguous interaction restraints
    • hbonds.tbl Unambiguous restraints
  • An analysis directory named ana_script that contains:

    • target.pdb Reference complex structure with renumbered atoms and renamed chainID that matches HADDOCK output
    • cluster-fnat.csh fraction-native.csh i-rmsd_to_xray.csh l-rmsd_to_xray.csh run_all-no-it0.csh make-target-files.csh run_all.csh run_all-dockQ.csh run_dockQ.csh All required scripts for the analysis
    • target.contacts10 target.izoneA target.contacts5 target.izoneB target.izone target.lzone All required files for the analysis:

1.2. Each XXXX_peptide folder contains:

  • HADDOCK-ready files:

    • peptide_beta.pdb Pymol generated PDB with ligand in a beta-sheet conformation
    • peptide_polypro.pdb Pymol generated PDB with ligand in a polyproline conformation
    • pdb.list List of ligand PDBs for step2 of cyclisation
    • XXX_peptide_XXXw.pdb Unbound ligand PDB (HADDOCK output from step2 of cyclisation)
    • step3_pdb.list List of ligand PDBs for step3 of cyclisation
  • Distance restraints file:

    • unambig.tbl Unambiguous cyclisation restrains

2. Docking results

Results of the 50STR_COMB docking protocol can be found on SBGrid: