HADDOCK2.4 web server protocol data

This repository provides the data files for performing the HADDOCK2.4 web server protocols described in the following manuscript:

• Honorato R.V., Giulini M., Reys V., Trellet M.E., Jiménez-García B., Schaarschmidt J., Koukos P.I., Rodrigues J.P.G.L.M., Karaca E., van Zundert, G., Roel-Touris J., van Noort, C.W., Jandová Z., Melquiond A.S.J. and Bonvin A.M.J.J. The HADDOCK2.4 web server: A leap forward in integrative modelling of biomolecular complexes. To be submitted (2023)

Input data, reference structures and HADDOCK parameter file (json) are provided for the following protocols:

1. Modeling of an antibody-antigen complexes using a priori NMR information defining the epitope on the antigen and the knowledge of the hypervariable loops on the antibody
2. Coarse-grained protein docking on a nucleosome particle: PRC1 ubiquitination module bound to the Nucleosome

The content of the two directories is the following:

antibody-antigen

• 4G6K_clean.pdb: HADDOCK-ready, pre-processed unbound form of the antibody
• 4I1B_clean.pdb: HADDOCK-ready, pre-processed unbound form of the antigen
• 4G6M_clean.pdb: Pre-processed reference structure of the complex to allow for easy comparison with the HADDOCK models
• job_params.json: The HADDOCK2.4 server parameter file corresponding to the described protocol. This file can be used for direct submission to the submit file interface of the server.

A full run result page for this system is available at: https://wenmr.science.uu.nl/haddock2.4/result/4242424242/264063-Antibody-Antigen-NMR

nucleosome

• 4r8p_clean.pdb: HADDOCK-ready, pre-processed nucleosome structure (bound form)
• 3rpg_clean.pdb: HADDOCK-ready, pre-processed unbound form of the PRC1 ubiquitination module
• 4r8p_reference.pdb: Pre-processed reference structure of the complex to allow for easy comparison with the HADDOCK models
• job_params.json: The HADDOCK2.4 server parameter file corresponding to the described protocol. This file can be used for direct submission to the submit file interface of the server.
• histones-passive.list: ASCII text file containing the list of solvent accessible residue on the nucleosme side used to define the passive residues for docking
• lys-cys-linkage.tbl: CNS-formatted distance restraint file for the defineing the CYS (PRC1) to LYS (nucleosome) linkage (ambiguously defined to two LYS residues)

A full run result page for this system is available at: https://wenmr.science.uu.nl/haddock2.4/result/4242424242/264564-Nucleosome-Docking-CG