RDKit for Rosetta: PLP ligand space as an example

Docking requires a molecule to dock. Preparing a ligand is often tricky, especially if the ligand is complicated, such as PLP. PLP is an interesting cofactor as it catalyses the reaction while the protein chooses the ligand. It binds tightly to the active site via its phosphate and its pyridine ring, while the metabolite to be transformed forms a Schiff base with it. Therefore, one would think that it makes easy to explore chemistry space with it. However, several technical hurdles are encountered, making it quite didactic.

Toasty CSS with BS4

In Bootstrap 4 you can have appear small alert-like rectangles, called toasts. However, getting these to work like notifications on top of the page in the top right is not trivial as it requires some CSS trickery. Here is what is required.

Pictograms with Plotly and FontAwesome

Plotly is one of the most powerful graphing packages for Python, JS and Julia. The cool feature is that the graphs are HTML bases with interactive graphs as opposed to a static jpg. There are several graphs that are missing, one of which is a pictogram. It's not a very silly graph, but  Luckily a pictogram is easy-ish to make.