Hi there,

This is a new set of very few WUs that are a collaboration with colleague of our lab. They are simply long equilibrations of homology modeled structures.
Protein structure data can either come from X-ray difraction studies (so called "crystal structures"), Nuclear magnetic ressonance (NMR) or by modelling them to already existing crystal structures ("homology model"). Sometimes we need to work with proteins for which there aren't crystal structures, which means that their 3D structure is unknown. In these cases, there are methods to infere the spatial organization of these 'face-less' proteins from similar (in aminoacid sequence) already crystallized proteins.
However, these homology models often need to be equilibrated for long times (hundreds of nanoseconds - each WU being now ~5 ns) with MD simulations to stabilize their structures before doing anything to them. Once the protein looks structurally equilibrated, we can start working with them.

Pretty much like a warm-up before jogging!

Cheers,
ignasi

Protein structure data can either come from X-ray difraction studies (so called "crystal structures") or by modelling them to already existing crystal structures ("homology model").

Don't forget NMR :)

Sure, thanks. Edited.