Cyclic-peptide-docking-benchmark

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

DOI: https://doi.org/10.1021/acs.jctc.2c00075

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

The list of peptides for the cyclic backone and disulphide bridge cyclic peptide sets can be found in the backbone-dataset.tsv and disulphide-dataset.tsv files

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: https://data.sbgrid.org/dataset/912