Linker definition

[nignatiadis]

Beyond definition of domain boundaries, eventually think about exact definition of linkers.

Right now: Linker is just the region between 2 consecutive NRP domains [or possibly region between start of protein and start of domain]

What if for example NRP domain is followed by non-NRP domain? Then linker would be huge with current definition..

Possible solutions: 1) use some other tool to actually identify linkers?
2) use pfam-A database to also search for non-NRP domains with sole purpose of being able to decide on linker length?
3) set max bound for different linker lengths and cut-off at this value?

[lorenzadlung]

Indeed a valuable point. First, I would go for option 3) since it is computationally least costly. But we can keep our eyes open for additional tools or once also check how performance of the designer would change if we include pfam search for all possible protein domains.