Hi,

if there is any information about residues critical for interaction with alpha-synuclein, you can use that information to validate your docking poses.

You can use PLIP https://plip-tool.biotec.tu-dresden.de/plip-web/plip/index to analyze your scores.

Which form of alpha-synuclein protein are you docking against? Large parts of this protein are thought to be intrinsically disordered and only assume a more defined structure upon interactions with other proteins, oligomerization or assembly into amyloid fibrils.

Thank You All. Annemarie Honegger Prof Ma am targeting the oligomers of the protein and I got the PDB ID as 1XQ8 from different literatures as well as from PDB. So I did pharmacophore modelling, virtual screening and molecular docking study against this protein using more than 800k ligands and I was able to retrieved 100 that matched my model, but validation of the docking scores is difficult since it has no co-crystallized ligands. Hoping I am in the right track.

Predictions are always much harder if you do not already know the answer! There are things you can do to assess whether the docked poses are reasonable, but the final verification has to be experimental!

You can plot the energy score of the different docked poses against the RMSD from the pose with the best score (instead of an experimental complex) to see whether there is a significant energy gap between the solutions with low RMSD to the best one and next-best solutions with significantly higher RMSD.

1XQ8 is a monomer, not an oligomer. Did you in any way model an assembly based on this?

How did you account for the fact that the alpha-helical (structured) part of 1XQ8 is predicted to be embedded in the lipid micelle, while the solvent-exposed tail is highly flexible, and the pdb file provides only an averaged NMR structure, rather than several conformations that fit the observed NMR signals (see fig.4 of https://www.jbc.org/article/S0021-9258(19)62979-0/fulltext ) ? I would assume that anything binding to the flexible part would bind through an induced fit. For a look at individual NMR models, look at all states of 2KKW.

If you dock to the protein only, be aware that anything that seems to bind to the hydrophobic, helical part would, in real life, have to compete with the lipids of the membrane/micelle.

By experiment.

I would recommend very short (10 - 50 ns; Gromacs, 5-10 in Amber) MD simulations followed by MMPBSA. I think redocking also adds up some piece of information about predictive power of the computing tools and choices…

Samee Ullah , and Edward Ntim Gasu should that MDS used as a docking validation, be repeated 3 independent runs?

Thank you all and Samee Ullah