Tuesday, 27 July 2021

What to look out for with an AlphaFold2 model

There is nothing more disheartening than telling someone "Sorry, I cannot help you with your protein, because no homologue structures of your protein are solved and any model will be rubbish". Now, with AlphaFold2 proteome release this is no longer the case. Or mostly: in fact there are several pitfalls and issues that need to be looked at, because the algorithm does not account for three things: binding partners and ligands, oligomerisation and alternate conformations.

Wednesday, 7 July 2021

Per residue RMSD

Recently I calculated the local RMSD caused by each residue and I thought I'd share the methods I used using PyRosetta —it is nothing at all novel, but I could not find a suitable implementation. The task is simple given two poses, find out what residue's backbone is changing the most by scanning along comparing each a short peptide window from each.