This repository contains all necessary information and scripts to do protein-peptide docking in HADDOCK, using the complex 1CZY as an example, which is the Supplementary Information for paper[reference]. For the usage of these files and scripts, please check the content of the paper[reference].

Note that the provided scripts are in principle generic and can be used for other systems as well.

This repository contains following folders and files:

• reference_complex.pdb, the crystal structure of the protein-peptide complex used as reference, which is chain A and D of 1CZY.
• protein.pdb, the crystal structure of unbound protein used for docking, which is chain C of 1CZZ.
• peptide_alpha.pdb, the alpha-helix conformation of peptide.
• peptide_polypro.pdb, the polyproline-II conformation of peptide.
• peptide_extended.pdb, the extended conformation of peptide.
• protein_active_residues.dat, the list of active residues of protein.
• peptide_passive_residues.dat, the list of passive residues of peptide.
• protein_histidine_states.dat, the list of charged states of Histidines in protein.
• structures.list, the list of 33 conformations or structures of peptide used for docking.

- md_1.pdb ... md_30.pdb, the 30 structures of peptide from MD simulations.

• vacuum.mdp, MD parameters for energy minimization in vacuum.
• ions.mdp, MD parameters for energy minimization in the presence of solvent and ions.
• nvt.mdp, MD parameters for energy minimization in constant volume conditions.
• npt.mdp, MD parameters for energy minimization in constant pressure conditions.
• unrestrained.mdp, MD parameters for energy minimization without any restraints.
• production.mdp, MD parameters for final production MD simulation.

• restraints.tbl, the AIRs file.
• new.html, the file to start a new HADDOCK project.

-build_seq.py, PyMOL script to build protein structure from sequence.

• automd.sh, bash script to prepare files and perform MD simulations using GROMACS.
• dpca.sh, bash script to do dihedral PCA using GROMACS.

• molprobity.py, python script to define charge states of histidines.

C. Geng, S. Narasimhan, João P.G.L.M. Rodrigues and Alexandre M.J.J. Bonvin, Information-driven, ensemble flexible peptide docking using HADDOCK, Modeling of peptide-protein interactions, Methods in Molecular Biology series (Springer Press), 2016