We provide here a number of link to tutorials illustrating the use of various WeNMR portals.
Table of contents
- Online tutorials
- Online lectures
- The 3D-DART user manual provides a step-by-step explanation of all settings available at every step of the DNA modeling process.Example projects ready for download as well as pre-loaded web forms are used to better explain several of the core functions.### CS-ROSETTA
- CS-Rosetta web server tutorial: This tutorial provides a step-by-step explanation of all settings available at every step of the 3D structure generation process. Example projects ready to be downloaded as well as pre-loaded web forms are used to better explain several of the core functions of the CS-ROSETTA portal.
- 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).
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.
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.
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 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 with the AMBER package: A tutorial about structure refinement using Restrained Molecular Dynamics (RMD) with the AMBER package.
RMD with RDC’s
- RMD with RDC’s: A tutorial about Restrained Molecular Dynamics (RMD) refinement of structures including RDC’s.
RMD including disulfide bonds
- RMD refinement with disulfide bonds: A tutorial about refinement of structures with Restrained Molecular Dynamics (RMD) and including disulfide bonds.
- The SPOTON user manual provides a short explanation of the simple input and output data of the SPOTON server.
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