Services for the European Open Science Cloud

HADDOCK2.4 basic protein-protein docking tutorial

E.g., 07/08/2020
E.g., 07/08/2020
When using the filter, please use both 'start' and 'end' fields

This section provides a list of training materials being used during the EOSC-hub training events.


This tutorial will demonstrate the use of HADDOCK for predicting the structure of a protein-protein complex from NMR chemical shift perturbation (CSP) data. Namely, we will dock two E. coli proteins involved in glucose transport: the glucose-specific enzyme IIA (E2A) and the histidine-containing phosphocarrier protein (HPr).

The structures in the free form have been determined using X-ray crystallography (E2A) (PDB ID 1F3G) and NMR spectroscopy (HPr) (PDB ID 1HDN). The structure of the native complex has also been determined with NMR (PDB ID 1GGR).

These NMR experiments have also provided us with an array of data on the interaction itself (chemical shift perturbations, intermolecular NOEs, residual dipolar couplings, and simulated diffusion anisotropy data), which will be useful for the docking. For this tutorial, we will only make use of inteface residues identified from NMR chemical shift perturbation data as described in Wang et al, EMBO J (2000).

Date created: 
Monday, July 1, 2019
Data modified: 
Tuesday, September 17, 2019