#PYMOL TUTORIAL 10 ANSWER REGISTRATION#
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Passive residues are those that contribute for the interaction, but are deemed of less importance. Throughout the simulation, these active residues are restrained to be part of the interface, if possible, otherwise incurring in a scoring penalty. Generally, active residues are those of central importance for the interaction, such as residues whose knockouts abolish the interaction or those where the chemical shift perturbation is higher. AIRs are defined through a list of residues that fall under two categories: active and passive. These allow the translation of raw data such as NMR chemical shift perturbation or mutagenesis experiments into distance restraints that are incorporated in the energy function used in the calculations. Moreover, the intimate coupling with CNS endows HADDOCK with the ability to actually produce models of sufficient quality to be archived in the Protein Data Bank.Ī central aspect to HADDOCK is the definition of Ambiguous Interaction Restraints or AIRs.

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What distinguishes HADDOCK from other docking software is its ability, inherited from CNS, to incorporate experimental data as restraints and use these to guide the docking process alongside traditional energetics and shape complementarity. HADDOCK (see ) is a collection of python scripts derived from ARIA ( ) that harness the power of CNS (Crystallography and NMR System – ) for structure calculation of molecular complexes.

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Use for this the following registration page. In order to run this tutorial you will need to have the following software installed: PyMOL.Īlso, if not provided with special workshop credentials to use the HADDOCK portal, make sure to register in order to be able to submit jobs. It! This an instruction prompt: follow it! This is a PyMOL prompt: write this in the Throughout the tutorial, coloured text will be used to refer to questions or The HADDOCK web server for data-driven biomolecular docking. The HADDOCK2.2 webserver: User-friendly integrative modeling of biomolecular complexes. 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).įor this tutorial we will make use of the H ADDOCK2.2 webserver.Ī description of our web server can be found in the following publications: 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.

The structure of the native complex has also been determined with NMR (PDB ID 1GGR).

#PYMOL TUTORIAL 10 ANSWER FREE#

The structures in the free form have been determined using X-ray crystallography (E2A) (PDB ID 1F3G) and NMR spectroscopy (HPr) (PDB ID 1HDN). coli proteins involved in glucose transport: the glucose-specific enzyme IIA (E2A) and the histidine-containing phosphocarrier protein (HPr). This tutorial will demonstrate the use of HADDOCK for predicting the structure of a protein-protein complex from NMR chemical shift perturbation (CSP) data.

Comparison with the reference structure.

Inspecting and preparing HPR for docking.

Inspecting and preparing E2A for docking.

This tutorial consists of the following sections:

Pymol tutorial 10 answer