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WeNMR is a worldwide e-Infrastructure for NMR and structural biology

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WeNMR Tutorials

We provide here a number of link to tutorials illustrating the use of various WeNMR portals.

Table of contents



Online tutorials

DISVIS

  • DisVis web server tutorial: A small introduction into DisVis to analyse the interaction space between two molecules from a set of restraints. It can help to filter out putative false positive restraints and predict key residues involved in the interaction from this set of restraints. It makes use of our web portal (does not require Linux).

Tutorials for HADDOCK version 2.4

  • HADDOCK2.4 basic protein-protein docking tutorial: A tutorial demonstrating the use of the HADDOCK web server to model a protein-protein complex using interface information derived from NMR chemical shift perturbation data. This tutorial does not require any Linux expertise and only makes use of our web server and PyMol for visualisation/analysis.

  • HADDOCK2.4 MS cross-links tutorial: A tutorial demonstrating the use of cross-linking data from mass spectrometry to guide the docking in HADDOCK. This tutorial builds on our DisVis tutorial and illustrates various scenarios of using cross-linking data in HADDOCK. This tutorial does not require any Linux expertise and only makes use of our web server and PyMol for visualisation/analysis.

  • DISVIS/HADDOCK2.4 oligomer puzzle: In this tutorial you will have to solve an oligomer puzzle, namely predicting the correct oligomeric state of a symmetrical homomer complex based on a few (artificial) cross-links. The tutorial does not require any Linux expertise and only makes use of the DISVIS and HADDOCK web servers and PyMol for visualisation/analysis.

  • HADDOCK2.4 CA-CA restraints guided docking tutorial: A tutorial demonstrating a template-based approach to model protein-protein complexes. It combines the PS-HomPPI web server to find suitable templates and generate CA-CA distance restraints and HADDOCK for the CA-CA guided modelling. This tutorial does not require any Linux expertise and only makes use of the PS-HomPPI and HADDOCK web servers and PyMol for visualisation/analysis.

  • HADDOCK2.4 ab-initio, multi-body symmetrical docking tutorial: A tutorial demonstrating multi-body docking with HADDOCK using its ab-initio mode with symmetry restraints. It is based on a former CASP-CAPRI target (T70).

  • HADDOCK2.4 ligand binding site tutorial: A tutorial demonstrating the use of HADDOCK in ab-initio mode to screen for potential ligand binding sites. The information from the ab-initio run is then used to setup a binding pocket-targeted protein-ligand docking run. We use as example the multidrug exporter AcrB.

  • HADDOCK2.4 antibody-antigen docking tutorial: This tutorial demonstrates the use of HADDOCK2.4 for predicting the structure of an antibody-antigen complex using information about the hypervariable loops of the antibody and either the entire surface of the antigen or a loose definition of the epitope. This tutorial does not require any Linux expertise and only makes use of our web servers and PyMol for visualisation/analysis.

Tutorials for HADDOCK version 2.2

  • HADDOCK basic protein-protein docking tutorial: A tutorial demonstrating the use of the HADDOCK web server to model a protein-protein complex using interface information derived from NMR chemical shift perturbation data. This tutorial does not require any Linux expertise and only makes use of our web server and PyMol for visualisation/analysis.

  • HADDOCK MS cross-links tutorial: A tutorial demonstrating the use of cross-linking data from mass spectrometry to guide the docking in HADDOCK. This tutorial builds on our DisVis tutorial and illustrates various scenarios of using cross-linking data in HADDOCK. This tutorial does not require any Linux expertise and only makes use of our web server and PyMol for visualisation/analysis.

  • DISVIS/HADDOCK oligomer puzzle: In this tutorial you will have to solve an oligomer puzzle, namely predicting the correct oligomeric state of a symmetrical homomer complex based on a few (artificial) cross-links. The tutorial does not require any Linux expertise and only makes use of the DISVIS and HADDOCK web servers and PyMol for visualisation/analysis.

  • HADDOCK CA-CA restraints guided docking tutorial: A tutorial demonstrating a template-based approach to model protein-protein complexes. It combines the PS-HomPPI web server to find suitable templates and generate CA-CA distance restraints and HADDOCK for the CA-CA guided modelling. This tutorial does not require any Linux expertise and only makes use of the PS-HomPPI and HADDOCK web servers and PyMol for visualisation/analysis.

  • HADDOCK ab-initio, multi-body symmetrical docking tutorial: A tutorial demonstrating multi-body docking with HADDOCK using its ab-initio mode with symmetry restraints. It is based on a former CASP-CAPRI target (T70).

  • HADDOCK ligand binding site tutorial: A tutorial demonstrating the use of HADDOCK in ab-initio mode to screen for potential ligand binding sites. The information from the ab-initio run is then used to setup a binding pocket-targetet protein-ligand docking run. We use as example the multidrug exporter AcrB.

Powerfit tutorial

  • PowerFit web server tutorial: A small introduction into PowerFit to automatically place a high-resolution atomic structure in a lower-resolution cryo-electron microscopy density map making use of our web portal (does not require Linux).

Integrative modelling of the RNA polymerase III apo complex

A combination of our DISVIS, POWERFIT and HADDOCK2.4 portals using cross-links and cryo-EM data to model a large macromolecular assembly. The tutorial is available here

How to use SAXS data in scoring HADDOCK decoys

A tutorial which shows how to make use of SAXS data in HADDOCK.

CS-HADDOCK

A re-scoring method that uses chemical shift data quantitatively to score HADDOCK models.

POWERFIT

  • PowerFit web server tutorial: A small introduction into PowerFit to automatically place a high-resolution atomic structure in a lower-resolution cryo-electron microscopy density map making use of our web portal (does not require Linux).

RMD-AMBER

  • RMD with the AMBER package: A tutorial about structure refinement using Restrained Molecular Dynamics (RMD) with the AMBER package.

  • RMD with RDC’s: A tutorial about Restrained Molecular Dynamics (RMD) refinement of structures including RDC’s.

  • RMD refinement with disulfide bonds: A tutorial about refinement of structures with Restrained Molecular Dynamics (RMD) and including disulfide bonds.

SPOTON

  • The SPOTON user manual provides a short explanation of the simple input and output data of the SPOTON server.



Online lectures

  • Various lectures on WeNMR-related services can be found on the WeNMR/WestLife YouTube channel.

  • Recording of a three hours lecture about HADDOCK by Alexandre Bonvin given on June 8th 2018 at NMRFAM, University of Wisconsin, Madison, USA:

      View recorded lecture

  • Recording of a lecture of Prof. Bonvin at the CECAM BImMS 2019 workshop in Lugano (Oct. 7th, 2019):

      View recorded lecture

  • Live demo of the HADDOCK2.4 thematic service. This demo given at the EOSC-Hub week 2020 conference shows in particular how to setup a refinement run in HADDOCK2.4 to assess the impact of a mutation, using the interaction between SARS-CoV2 RBD domain and a peptide extracted from the ACE2 receptor as an example.

      View demo