Jupyter Notebook Gallery

The notebooks can be accessed locally by issuing:

mdc_notebooks.py

from the CLI. This will create a local “sandboxed” copy of the notebooks, which you can modify and play around with without breaking the original notebooks. Note: the Covid notebooks are not shipped with mdciao.

Tutorials

One single notebook providing an overview of mdciao

FAQs

These are issue-specific notebooks. They are more verbose and explore how particular optional parameters affect the output of some methods.

Missing Contacts	Comparing Frequencies: Bar Plots
Controlling Flareplots: Schemes	Comparing Frequencies: Flareplots

Examples

These are worked out examples from the real world, from raw data to final results. They are the best starting point to copy and modify with your own data.

Interfaces: β2 Adrenergic Receptor in Complex with Empty Gs-Protein	Binding-Pockets: EGFR Kinase Inhibitors
Covid-19 Spike Protein Example 1: Residue Neighborhoods	Covid-19 Spike Protein Example 2: Molecular Interfaces
3D Multiple Sequence Alignment via Consensus Labels on μ-Opioid Receptor, β2 Adregneric Receptor, Opsin, and Dopamine D1 Receptor	Contact Frequencies for multiple systems via consensus labels