Basic knowledge of the Linux command line.
This workshop consists of a series of Jupyter notebooks:
- Basic Analysis: An introduction to interactive MD data analysis with Jupyter notebooks and MDTraj.
- PCA Analysis: An introduction to the use of Principal Component Analysis methods for the analysis of sampling and convergence of MD simulations.
- Statistical Analysis: An introduction to the use of statistical methods to assess the significance of data extracted from MD simulations.
- Ubiquitin Analysis: Application of some of the methods in the other notebooks to the analysis of data from an MD simulation of ubiquitin.
- Prokpka Analysis: Analysis of a PDB structure using Propka to predict protonation states of acidic and basic residues.
- Procheck Analysis: A slightly more advanced notebook that demonstartes how you can automate the Procheck analysis of a multi-model PDB file of an NMR-derived protein structure.
These can be run using the
CCPBioSim workshop server.
Once you have started the server, navigate to the md_workshop
directory and you will find the
notebooks there.
If you want to take a copy for your own use back home, the simplest approach is to clone this repository:
git clone https://github.com/CCPBioSim/md_workshop.git