Tutorials#
GB3 domain how-to for MD beginners#
Running MD simulation of the GB3 domain and computing a SAXS curve.
Here you find shell scripts that automatically
set up and run an MD simulation of the GB3 domain,
of a pure-water box,
and compute the SAXS curve.
Download the tar package GB3-SAXS-tutorial.tar, unpack (tar xf GB3-SAXS-tutorial.tar), and look at the README and bash files. These scripts are also a good starting point for automating explicit-solvent SAXS calculations. For more detailed explanations, please see the other tutorials.
Computing a SAXS curve, a step by step guide#
Here you find a step by step guide for how to compute a SAXS curve from a given MD simulation of a biomolecule, together with a template parameter file.
SAXS/SANS predictions, SAXS-driven MD, and multi-replica ensemble refinement#
This tutorial shows the following:
Computing SAXS/SANS curves from a given protein trajectory
SAXS-driven simulations: opening a two-domain protein
Multi-replica SAXS-restrained ensemble simulations of an intrinsically disordered protein
Tutorial carried out at the EMBO SAS workshop in Grenoble.
SAXS and SANS curves of a protein-detergent complex#
Small-angle X-ray Scattering (SAXS) is increasingly popular method to study biomolecules in solution, that is under near-native conditions. Its sister method, Small-angle Neutron Scattering (SANS), is popular since it allows so-called contrast variation experiments by measuring at different D2O concentrations in the buffer, allowing one to obtain structural information on different components of the biomolecular complexes (such as on different protein domains, RNA versus protein in protein/RNA complex, protein versus detergent in a protein/detergent complex, etc.). In this tutorial, we show how to compute SAXS and SANS curves of a protein-detergent complex.
