1/4/2024 0 Comments Dock it solves proteinThis is followed by a rigid body energy minimization step, where the partners are allowed to rotate and translate to optimize the interaction. The partners are separated in space and rotated randomly about their centres of mass. In this initial stage, the interacting partners are treated as rigid bodies, meaning that all geometrical parameters such as bonds lengths, bond angles, and dihedral angles are frozen. Randomization of orientations and rigid-body minimization (it0) The docking protocol of HADDOCK was designed so that the molecules experience varying degrees of flexibility and different chemical environments, and it can be divided in three different stages, each with a defined goal and characteristics:ġ. Hence, a careful selection of which residues are active and which are passive is critical for the success of the docking. If such a residue does not belong in the interface there is no scoring penalty. 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. 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. Use for this the following registration page. In order to run this practical 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. You are expected to submit a report providing answers to all questions throughout this tutorial. This is a question prompt: try answering it! This an instruction prompt: follow it! This is a PyMOL prompt: write this in the PyMOL command line prompt! Throughout the practical, coloured text will be used to refer to questions or instructions, and/or PyMOL commands. The HADDOCK web server for data-driven biomolecular docking. The HADDOCK2.2 webserver: User-friendly integrative modeling of biomolecular complexes. For this tutorial, you 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 you will make use of the HADDOCK2.4 webserver.Ī description of the previous major version of our web server HADDOCK2.2 can be found in the following publications: These NMR experiments have also provided us with an array of data on the interaction itself. The structure of the native complex has also been determined with NMR (PDB ID 1GGR). 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 practical 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.Submission and validation of structures.Inspecting and preparing HPR for docking.Inspecting and preparing E2A for docking.This computer practical consists of the following sections:
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