Crosslink Residue Selection for AlphaLink 2

[jimfeng9705]

Hello,

Would it make sense to limit/select the crosslink-reactive residues for AlphaLink 2? For example, while DSBU primarily targets lysine residues, it can also react with serine, threonine, and tyrosine. Depending on the search algorithm, these additional residues could contribute a significant number of crosslinks.

We've noticed that including all potential crosslinks in the input file can negatively impact scoring metrics (e.g., pTM) and result in suboptimal docking geometries for the protein complex.

Thanks,

[lhatsk]

I think it will depend very much on your target. In general, I would use as much information as possible. If the result is not satisfying, removing links, e.g., intra-chain links in case of homomers or links from disordered regions seems to help and will likely also increase diversity.