haddocking
Possible upd for SBM course
- Suggest to bring a mouth for the pymol
- During the linux session make sure students read about environmental variables, cat, nano (or vim)
- Encourage students to not be afraid of errors
precalculated results are un-capped, so it is not possible to merge trajectories with student’s capped runs
Aproximate schedule to show on the 1st day Monday: set up, familiarize with Linux Tuesday: Homology Wednesday-Friday: start MD production Monday-Tuesday: analyze MD run Wednesday: docking Thursday: analyse docking results & start report Friday: report
Ask students to make haddock account on first Monday. Aks students to request guru on second Monday (they are sad they have to wait now)
Point to all the plots generated during clustering the trajecories - to help to pick 5 representatives out of all 10-15 clusters
Note:
- sometimes peptide can stretch over the given dimention of a box. In this case, it’s size have to be inceased.
- carefull with disordered part of MDM2 covering the binding side for p53
Pay attention to SA of active residues predicted with ARCTIC-3D!
What is SA ?
Pay attention to SA of active residues predicted with ARCTIC-3D!
What is SA ?
Surface accessibility. There’s no guarantee that ARCTIC-3D-predicted resideus are surface accessible!
In fact, with Irem we realized that two of ARCTIC-3D-predicted residues that we used as active are almost fully buried.
UPD: while haddock web will filter out non-assessible residues by itself, it’s still nice to be aware of, e.g. for the students to have an idea of exactly how many active residues are guiding the docking